Dear Amber users:
I'm confused why does the H3O+ and H2O exist electrostatic energy. The related prmtop and inpcrd (whose original prep and frcmod files were dowload from the
http://www.pharmacy.manchester.ac.uk/bryce/amber )are added to the attachment the results calculated by sander module of Amber are as follows:
H2O:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 3.6676E+01 1.5945E+01 3.2183E+01 H1 2
BOND = 0.0896 ANGLE = 0.0000 DIHED = 0.0000
VDWAALS = 0.0000 EEL = 36.5866 HBOND = 0.0000
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
H3O+:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.8080E+02 2.6283E+01 5.2810E+01 H2 3
BOND = 0.2262 ANGLE = 0.0000 DIHED = 0.0000
VDWAALS = 0.0000 EEL = 180.5715 HBOND = 0.0000
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
At the same time I have used the printBonds command to ensure the bonds are bonded to the oxgens so as the follow situations:
H2O:
Atom 1 Atom 2 R eq Frc Cnst
1 O1 ( OW) 2 H1 ( HW) 0.9570 553.0000
1 O1 ( OW) 3 H2 ( HW) 0.9570 553.0000
H3O:
Atom 1 Atom 2 R eq Frc Cnst
1 O1 ( OW) 2 H1 ( HW) 0.9570 553.0000
1 O1 ( OW) 3 H2 ( HW) 0.9570 553.0000
1 O1 ( OW) 4 H3 ( HW) 0.9570 553.0000
Now, I need you to help me to slove the doubt and thanks for your help.
------------------ Original ------------------
From: "amber-request";<amber-request.ambermd.org>;
Date: Wed, Apr 9, 2014 03:00 AM
To: "amber"<amber.ambermd.org>;
Subject: AMBER Digest, Vol 818, Issue 1
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AMBER Mailing List Digest
Today's Topics:
1. Re: antechamber (David A Case)
2. Re: Really Weird Problem with Replica Exchange (Carlos Simmerling)
3. Re: Really Weird Problem with Replica Exchange
(Christopher A Thiebaut)
4. Re: Really Weird Problem with Replica Exchange
(Christina Bergonzo)
5. Re: Really Weird Problem with Replica Exchange
(Christopher A Thiebaut)
6. Re: antechamber (Lara rajam)
7. Re: antechamber (Jason Swails)
8. REMD with pmemd.cuda (Milo Westler)
9. number of ions (integral) too much in RDF plot (Jio M)
10. About the error "Unable to correctly identify element CU" in
QMMM simulation (Yeng-Tseng Wang)
11. When I run the pmemd.cuda, sometimes computer will be
rebooted. (KangMooseok)
12. error in reading protein file (Arunima Shilpi)
13. When I run the pmemd.cuda, sometimes computer will be
rebooted.?? (KangMooseok)
14. error in loading protein (Arunima Shilpi)
15. Re: error in loading protein (Soumendranath Bhakat)
16. Re: REMD with pmemd.cuda (Nhai)
17. Karplus J-coupling (Neha Gandhi)
18. Re: About the error "Unable to correctly identify element CU"
in QMMM simulation (Jason Swails)
19. Re: When I run the pmemd.cuda, sometimes computer will be
rebooted. (Jason Swails)
20. Re: error in reading protein file (Jason Swails)
21. Re: REMD with pmemd.cuda (Jason Swails)
22. Re: REMD with pmemd.cuda (Ashutosh Shandilya)
23. Re: Karplus J-coupling (David A Case)
24. Re: REMD with pmemd.cuda (Jason Swails)
25. number of ions (integral) too much in RDF plot (Jio M)
26. Re: REMD with pmemd.cuda (Ashutosh Shandilya)
27. error in input file /nmropt=1 (Urszula Uciechowska)
28. Re: error in input file /nmropt=1 (Asaminew Haile)
29. Re: error in input file /nmropt=1 with dist.RST
(Urszula Uciechowska)
30. Re: error in input file /nmropt=1 with dist.RST
(Urszula Uciechowska)
31. Re: error in input file /nmropt=1 (Brian Radak)
32. Questions about the energy of H3O+ ( jinfenghuang )
33. Re: REMD with pmemd.cuda (Milo Westler)
34. Re: Asking about using Vector Analysis: Thermo (Setyanto Md)
35. Re: Really Weird Problem with Replica Exchange
(Christina Bergonzo)
36. Re: REMD with pmemd.cuda (Milo Westler)
37. Re: REMD with pmemd.cuda (Jason Swails)
38. Re: antechamber (Lara rajam)
39. Re: Questions about the energy of H3O+ (Jason Swails)
40. Re: error in input file /nmropt=1 (David A Case)
41. Re: Asking about using Vector Analysis: Thermo (David A Case)
42. Re: REMD with pmemd.cuda (Milo Westler)
----------------------------------------------------------------------
Message: 1
Date: Mon, 7 Apr 2014 15:12:13 -0400
From: David A Case <case.biomaps.rutgers.edu>
Subject: Re: [AMBER] antechamber
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20140407191213.GD63139.biomaps.rutgers.edu>
Content-Type: text/plain; charset=us-ascii
On Mon, Apr 07, 2014, Lara rajam wrote:
> I was able to proceed with all the commands, but the topology file is not
> generated
>
> I have the following error
...your snippet didn't show any errors, just warnings. But there must have
been errors, so look carefully in the leap.log file.
>
> O -SO 0.00 0.000 ATTN, need revision
> SO-OS 0.00 0.000 ATTN, need revision
This looks odd, since the atom types are in upper case, but gaff atom types
are always lower case. There is almost certainly something wrong with the
structure, or with the ways in which antechamber is identifying atoms types:
did you ask for "-at amber"? (don't do that, unless you know your molecule
has just the sorts of functional groups found in proteins or nucleic acids.)
..good luck...dac
------------------------------
Message: 2
Date: Mon, 7 Apr 2014 15:48:18 -0400
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Subject: Re: [AMBER] Really Weird Problem with Replica Exchange
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAGk3s-QgkeP-SOhOXbtZa_1avqN1UjUy52xnYYMF=aUE=pZEjw.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
what were the initial structures? were they pre-equilibrated that the right
Ts? tell us more about how you got to this point...
On Mon, Apr 7, 2014 at 2:58 PM, Christopher A Thiebaut
<cthieba.purdue.edu>wrote:
> Helllo all,
>
> I am having what I imagine to be a very unusual problem running replica
> exchange of thermolysin solvated with explicit TIP3P water.
> The simulations will run without any error messages, but I am sure the
> results I am seeing are not meaningful because most replicas are exchanging
> at most exchange attempts and even more so because the volocity scaling is
> always 1.0 (meaning the volocites are not changed at all), except once
> during the first exchange. In addition, the total potential energy seems
> to be slowly increasing throughout the simulation which also should not be
> happening.
>
> Here's a sample of my rem.log file so you can see what I'm talking about:
> # Rep#, Velocity Scaling, T, Eptot, Temp0, NewTemp0, Success rate (i,i+1),
> ResStruct#
> # exchange 1
> 1 1.07 0.00-158275.28 270.00 310.44 0.00 -1
> 2 1.00 0.00-158841.35 271.23 272.47 2.00 -1
> 3 1.00 0.00-159708.30 272.47 271.23 0.00 -1
> 4 1.00 0.00-159547.14 273.71 274.96 2.00 -1
> 5 1.00 0.00-159457.82 274.96 273.71 0.00 -1
> 6 1.00 0.00-160730.25 276.21 277.46 2.00 -1
> 7 1.00 0.00-160858.37 277.46 276.21 0.00 -1
> 8 1.00 0.00-161155.52 278.73 279.98 2.00 -1
> 9 1.00 0.00-161044.87 279.98 278.73 0.00 -1
> 10 1.00 0.00-161039.89 281.25 282.53 2.00 -1
> 11 1.00 0.00-161096.24 282.53 281.25 0.00 -1
> 12 1.00 0.00-162494.74 283.81 285.09 2.00 -1
> 13 1.00 0.00-162767.85 285.09 283.81 0.00 -1
> 14 1.00 0.00-161902.49 286.38 287.68 2.00 -1
> 15 1.00 0.00-163145.99 287.68 286.38 0.00 -1
> 16 1.00 0.00-162901.03 288.97 290.28 2.00 -1
> 17 1.00 0.00-164106.69 290.28 288.97 0.00 -1
> 18 -1.00 0.00-163819.64 291.58 291.58 0.00 -1
> 19 -1.00 0.00-163549.67 292.90 292.90 0.00 -1
> 20 1.00 0.00-163950.79 294.21 295.53 2.00 -1
> 21 1.00 0.00-164690.76 295.53 294.21 0.00 -1
> 22 1.00 0.00-165187.80 296.86 298.19 2.00 -1
> 23 1.00 0.00-165377.17 298.19 296.86 0.00 -1
> 24 -1.00 0.00-164848.36 299.52 299.52 0.00 -1
> 25 -1.00 0.00-164797.83 300.86 300.86 0.00 -1
> 26 1.00 0.00-165237.92 302.21 303.56 2.00 -1
> 27 1.00 0.00-166216.65 303.56 302.21 0.00 -1
> 28 1.00 0.00-166127.19 304.91 306.27 2.00 -1
> 29 1.00 0.00-167327.09 306.27 304.91 0.00 -1
> 30 1.00 0.00-166545.00 307.64 309.01 2.00 -1
> 31 1.00 0.00-168071.75 309.01 307.64 0.00 -1
> 32 0.93 0.00-167178.34 310.44 270.00 2.00 -1
> ......................................................................
> # exchange 25
> 1 1.00 309.91-237311.34 309.01 307.64 0.08 -1
> 2 1.00 304.26-237005.16 302.21 303.56 1.04 -1
> 3 1.00 296.00-237356.49 296.86 298.19 1.04 -1
> 4 1.00 304.33-237213.57 304.91 306.27 0.96 -1
> 5 1.00 300.61-237074.41 299.52 300.86 0.96 -1
> 6 1.00 306.71-237010.94 307.64 309.01 0.88 -1
> 7 1.00 288.23-237533.96 286.38 287.68 1.04 -1
> 8 -1.00 309.85-237252.49 310.44 310.44 0.08 -1
> 9 1.00 289.99-237569.69 288.97 290.28 1.04 -1
> 10 1.00 307.03-237289.10 306.27 304.91 0.88 -1
> 11 1.00 296.78-237439.24 294.21 295.53 1.04 -1
> 12 1.00 302.80-237548.07 303.56 302.21 0.96 -1
> 13 1.00 291.19-237476.28 291.58 292.90 0.96 -1
> 14 1.00 298.13-237536.76 295.53 294.21 0.96 -1
> 15 1.00 284.22-237758.43 281.25 282.53 1.04 -1
> 16 1.00 291.28-237590.61 290.28 288.97 0.96 -1
> 17 1.00 277.07-237711.31 278.73 279.98 1.04 -1
> 18 1.00 277.52-237747.34 276.21 277.46 1.04 -1
> 19 1.00 300.95-237501.70 300.86 299.52 0.96 -1
> 20 1.00 297.03-237561.12 298.19 296.86 0.88 -1
> 21 1.00 282.63-237651.93 283.81 285.09 1.04 -1
> 22 -1.00 270.53-238135.36 270.00 270.00 0.56 -1
> 23 1.00 272.50-237928.60 271.23 272.47 0.88 -1
> 24 1.00 292.11-237641.94 292.90 291.58 0.96 -1
> 25 1.00 288.51-237686.39 287.68 286.38 0.96 -1
> 26 1.00 285.15-237838.02 285.09 283.81 0.96 -1
> 27 1.00 269.94-237998.93 272.47 271.23 0.72 -1
> 28 1.00 278.70-237910.14 279.98 278.73 0.96 -1
> 29 1.00 275.61-238021.61 274.96 273.71 0.96 -1
> 30 1.00 282.57-237916.92 282.53 281.25 0.96 -1
> 31 1.00 276.88-238031.26 277.46 276.21 0.96 -1
> 32 1.00 273.65-237788.60 273.71 274.96 0.96 -1
> # exchange 26
> 1 1.00 309.43-237528.66 307.64 306.27 0.85 -1
> 2 1.00 303.95-237551.08 303.56 304.91 1.00 -1
> 3 1.00 297.95-237809.91 298.19 299.52 0.92 -1
> 4 1.00 306.31-237657.13 306.27 307.64 0.92 -1
> 5 1.00 299.96-237577.66 300.86 302.21 1.00 -1
> 6 1.00 308.95-237472.73 309.01 310.44 0.15 -1
> 7 1.00 286.56-237844.08 287.68 288.97 1.00 -1
> 8 1.00 310.00-237519.31 310.44 309.01 0.08 -1
> 9 1.00 291.81-237729.64 290.28 291.58 1.00 -1
> 10 1.00 303.70-237715.75 304.91 303.56 0.92 -1
> 11 1.00 296.62-237700.83 295.53 296.86 1.00 -1
> 12 1.00 303.16-237772.77 302.21 300.86 1.00 -1
> 13 1.00 292.60-237770.36 292.90 294.21 1.00 -1
> 14 1.00 293.41-237816.24 294.21 292.90 1.00 -1
> 15 1.00 282.61-237999.04 282.53 283.81 1.00 -1
> 16 1.00 289.23-237958.84 288.97 287.68 1.00 -1
> 17 1.00 278.69-238016.41 279.98 281.25 1.00 -1
> 18 1.00 278.70-238051.34 277.46 278.73 1.00 -1
> 19 1.00 298.26-237923.06 299.52 298.19 0.92 -1
> 20 1.00 293.43-237819.98 296.86 295.53 1.00 -1
> 21 1.00 285.90-237872.36 285.09 286.38 1.00 -1
> 22 1.00 271.15-238192.37 270.00 271.23 0.62 -1
> 23 1.00 272.53-238207.17 272.47 273.71 0.77 -1
> 24 1.00 290.92-238028.52 291.58 290.28 0.92 -1
> 25 1.00 286.71-238159.73 286.38 285.09 1.00 -1
> 26 1.00 284.16-238189.10 283.81 282.53 1.00 -1
> 27 1.00 272.89-238264.83 271.23 270.00 0.85 -1
> 28 1.00 278.46-238289.12 278.73 277.46 1.00 -1
> 29 1.00 272.73-238268.68 273.71 272.47 0.92 -1
> 30 1.00 281.90-238206.67 281.25 279.98 1.00 -1
> 31 1.00 279.16-238218.60 276.21 274.96 1.00 -1
> 32 1.00 273.42-238084.44 274.96 276.21 1.00 -1
> # exchange 27
> 1 1.00 305.14-237896.37 306.27 304.91 0.89 -1
> 2 1.00 306.70-237688.11 304.91 306.27 0.96 -1
> 3 1.00 299.55-237906.46 299.52 300.86 0.96 -1
> 4 1.00 308.78-237779.85 307.64 309.01 0.89 -1
> 5 1.00 303.02-237740.95 302.21 303.56 1.04 -1
> 6 -1.00 312.04-237760.32 310.44 310.44 0.07 -1
> 7 1.00 289.44-238148.68 288.97 290.28 1.04 -1
> 8 1.00 308.40-237883.47 309.01 307.64 0.15 -1
> 9 1.00 293.62-238039.32 291.58 292.90 0.96 -1
> 10 1.00 303.22-237972.21 303.56 302.21 0.96 -1
> 11 1.00 298.26-238017.06 296.86 298.19 1.04 -1
> 12 1.00 302.52-238053.44 300.86 299.52 0.96 -1
> 13 1.00 297.91-238061.27 294.21 295.53 1.04 -1
> 14 1.00 293.39-238165.74 292.90 291.58 0.96 -1
> 15 1.00 286.69-238367.18 283.81 285.09 1.04 -1
> 16 1.00 285.33-238372.24 287.68 286.38 0.96 -1
> 17 1.00 280.09-238415.47 281.25 282.53 1.04 -1
> 18 1.00 279.14-238456.86 278.73 279.98 1.04 -1
> 19 1.00 297.69-238179.86 298.19 296.86 0.89 -1
> 20 1.00 293.78-238363.05 295.53 294.21 0.96 -1
> 21 1.00 286.04-238315.32 286.38 287.68 1.04 -1
> 22 1.00 269.92-238495.65 271.23 272.47 0.89 -1
> 23 1.00 272.51-238431.54 273.71 274.96 0.96 -1
> 24 1.00 289.51-238323.64 290.28 288.97 0.96 -1
> 25 1.00 285.80-238400.25 285.09 283.81 0.96 -1
> 26 1.00 284.11-238504.05 282.53 281.25 0.96 -1
> 27 -1.00 270.33-238639.41 270.00 270.00 0.59 -1
> 28 1.00 278.26-238633.26 277.46 276.21 0.96 -1
> 29 1.00 271.87-238758.14 272.47 271.23 0.74 -1
> 30 1.00 278.97-238406.37 279.98 278.73 0.96 -1
> 31 1.00 275.36-238642.13 274.96 273.71 0.96 -1
> 32 1.00 277.11-238336.79 276.21 277.46 1.04 -1
> # exchange 28
> 1 1.00 305.41-238178.28 304.91 303.56 0.93 -1
> 2 1.00 308.72-237888.75 306.27 307.64 0.93 -1
> 3 -1.00 299.85-238411.98 300.86 300.86 0.93 -1
> 4 1.00 308.47-237966.66 309.01 310.44 0.21 -1
> 5 1.00 302.86-237989.18 303.56 304.91 1.00 -1
> 6 1.00 310.64-238126.41 310.44 309.01 0.07 -1
> 7 1.00 291.09-238323.96 290.28 291.58 1.00 -1
> 8 1.00 306.54-238287.31 307.64 306.27 0.86 -1
> 9 1.00 292.28-238398.82 292.90 294.21 1.00 -1
> 10 -1.00 302.07-238374.29 302.21 302.21 1.00 -1
> 11 1.00 299.33-238367.94 298.19 299.52 0.93 -1
> 12 1.00 299.74-238329.33 299.52 298.19 0.93 -1
> 13 1.00 294.48-238329.94 295.53 296.86 1.00 -1
> 14 1.00 292.88-238512.89 291.58 290.28 0.93 -1
> 15 1.00 284.54-238592.77 285.09 286.38 1.00 -1
> 16 1.00 289.06-238586.60 286.38 285.09 1.00 -1
> 17 1.00 282.18-238604.33 282.53 283.81 1.00 -1
> 18 1.00 280.42-238498.62 279.98 281.25 1.00 -1
> 19 1.00 298.42-238339.10 296.86 295.53 1.00 -1
> 20 1.00 295.23-238501.82 294.21 292.90 1.00 -1
> 21 1.00 287.96-238622.69 287.68 288.97 1.00 -1
> 22 1.00 274.59-238791.23 272.47 273.71 0.79 -1
> 23 1.00 274.34-238732.39 274.96 276.21 1.00 -1
> 24 1.00 290.89-238503.91 288.97 287.68 1.00 -1
> 25 1.00 284.40-238719.97 283.81 282.53 1.00 -1
> 26 1.00 281.12-238697.12 281.25 279.98 1.00 -1
> 27 1.00 271.44-238981.93 270.00 271.23 0.64 -1
> 28 1.00 277.56-238877.61 276.21 274.96 1.00 -1
> 29 1.00 272.58-239072.51 271.23 270.00 0.86 -1
> 30 1.00 279.19-238902.86 278.73 277.46 1.00 -1
> 31 1.00 274.58-238952.80 273.71 272.47 0.93 -1
> 32 1.00 278.29-238672.97 277.46 278.73 1.00 -1
> # exchange 29
> 1 1.00 303.10-238482.53 303.56 302.21 0.97 -1
> 2 1.00 308.47-238268.33 307.64 309.01 0.90 -1
> 3 1.00 300.90-238576.50 300.86 299.52 0.90 -1
> 4 -1.00 310.92-238315.71 310.44 310.44 0.07 -1
> 5 1.00 304.45-238317.36 304.91 306.27 0.97 -1
> 6 1.00 307.80-238499.68 309.01 307.64 0.21 -1
> 7 1.00 291.95-238596.78 291.58 292.90 0.97 -1
> 8 1.00 306.74-238454.39 306.27 304.91 0.90 -1
> 9 1.00 294.77-238569.62 294.21 295.53 1.03 -1
> 10 1.00 303.24-238531.15 302.21 303.56 1.03 -1
> 11 1.00 299.01-238638.43 299.52 300.86 0.97 -1
> 12 1.00 299.36-238835.63 298.19 296.86 0.90 -1
> 13 1.00 298.09-238588.55 296.86 298.19 1.03 -1
> 14 1.00 291.63-238777.70 290.28 288.97 0.97 -1
> 15 1.00 286.85-239032.37 286.38 287.68 1.03 -1
> 16 1.00 285.69-238846.49 285.09 283.81 0.97 -1
> 17 1.00 282.94-238892.18 283.81 285.09 1.03 -1
> 18 1.00 281.44-238894.57 281.25 282.53 1.03 -1
> 19 1.00 296.81-238719.29 295.53 294.21 0.97 -1
> 20 1.00 293.05-238860.89 292.90 291.58 0.97 -1
> 21 1.00 286.63-238769.89 288.97 290.28 1.03 -1
> 22 1.00 276.10-238983.43 273.71 274.96 0.97 -1
> 23 1.00 278.03-238930.08 276.21 277.46 1.03 -1
> 24 1.00 286.91-238958.25 287.68 286.38 0.97 -1
> 25 1.00 282.26-239046.26 282.53 281.25 0.97 -1
> 26 1.00 279.78-239123.91 279.98 278.73 0.97 -1
> 27 1.00 273.78-239151.24 271.23 272.47 0.90 -1
> 28 1.00 275.98-239171.49 274.96 273.71 0.97 -1
> 29 -1.00 269.99-239317.35 270.00 270.00 0.62 -1
> 30 1.00 276.91-239191.40 277.46 276.21 0.97 -1
> 31 1.00 272.73-239255.54 272.47 271.23 0.76 -1
> 32 1.00 279.96-238888.03 278.73 279.98 1.03 -1
> # exchange 30
> 1 1.00 302.64-238842.01 302.21 300.86 1.00 -1
> 2 1.00 308.63-238427.17 309.01 310.44 0.27 -1
> 3 1.00 299.84-238911.95 299.52 298.19 0.93 -1
> 4 1.00 309.86-238515.73 310.44 309.01 0.07 -1
> 5 1.00 307.42-238560.64 306.27 307.64 0.93 -1
> 6 1.00 307.48-238702.43 307.64 306.27 0.87 -1
> 7 1.00 292.53-238839.87 292.90 294.21 1.00 -1
> 8 1.00 306.00-238777.41 304.91 303.56 0.93 -1
> 9 1.00 297.32-238947.72 295.53 296.86 1.00 -1
> 10 1.00 304.05-238883.82 303.56 304.91 1.00 -1
> 11 1.00 302.57-238780.54 300.86 302.21 0.93 -1
> 12 1.00 292.21-238910.66 296.86 295.53 1.00 -1
> 13 1.00 298.97-238780.23 298.19 299.52 0.93 -1
> 14 1.00 286.86-239171.01 288.97 287.68 1.00 -1
> 15 1.00 290.28-239150.80 287.68 288.97 1.00 -1
> 16 1.00 282.76-239323.47 283.81 282.53 1.00 -1
> 17 1.00 284.27-239063.46 285.09 286.38 1.00 -1
> 18 1.00 281.82-239049.67 282.53 283.81 1.00 -1
> 19 1.00 292.78-239024.98 294.21 292.90 1.00 -1
> 20 1.00 293.24-239149.18 291.58 290.28 0.93 -1
> 21 1.00 291.56-239013.66 290.28 291.58 1.00 -1
> 22 1.00 276.39-239397.26 274.96 276.21 1.00 -1
> 23 1.00 278.04-239172.39 277.46 278.73 1.00 -1
> 24 1.00 287.81-239189.88 286.38 285.09 1.00 -1
> 25 1.00 281.80-239499.51 281.25 279.98 1.00 -1
> 26 1.00 279.53-239167.74 278.73 277.46 1.00 -1
> 27 1.00 272.13-239418.19 272.47 273.71 0.80 -1
> 28 1.00 273.73-239459.18 273.71 272.47 0.93 -1
> 29 1.00 269.25-239534.80 270.00 271.23 0.67 -1
> 30 1.00 278.19-239456.51 276.21 274.96 1.00 -1
> 31 1.00 267.89-239471.35 271.23 270.00 0.87 -1
> 32 1.00 282.43-239161.13 279.98 281.25 1.00 -1
> # exchange 31
> 1 1.00 301.00-238974.09 300.86 299.52 0.90 -1
> 2 -1.00 309.61-238660.96 310.44 310.44 0.06 -1
> 3 1.00 299.18-239060.07 298.19 296.86 0.90 -1
> 4 1.00 310.05-238867.09 309.01 307.64 0.26 -1
> 5 1.00 305.97-238751.83 307.64 309.01 0.90 -1
> 6 1.00 303.80-238862.17 306.27 304.91 0.90 -1
> 7 1.00 294.92-239133.23 294.21 295.53 1.03 -1
> 8 1.00 300.79-239134.89 303.56 302.21 0.97 -1
> 9 1.00 295.27-239078.59 296.86 298.19 1.03 -1
> 10 1.00 307.38-238976.05 304.91 306.27 0.97 -1
> 11 1.00 299.93-239007.75 302.21 303.56 1.03 -1
> 12 1.00 296.23-239266.13 295.53 294.21 0.97 -1
> 13 1.00 300.31-238964.11 299.52 300.86 0.97 -1
> 14 1.00 288.87-239491.68 287.68 286.38 0.97 -1
> 15 1.00 288.87-239181.78 288.97 290.28 1.03 -1
> 16 1.00 283.85-239447.44 282.53 281.25 0.97 -1
> 17 1.00 286.93-239387.00 286.38 287.68 1.03 -1
> 18 1.00 285.28-239293.13 283.81 285.09 1.03 -1
> 19 1.00 294.38-239262.60 292.90 291.58 0.97 -1
> 20 1.00 291.41-239473.95 290.28 288.97 0.97 -1
> 21 1.00 291.99-239025.10 291.58 292.90 0.97 -1
> 22 1.00 277.99-239464.65 276.21 277.46 1.03 -1
> 23 1.00 280.21-239389.24 278.73 279.98 1.03 -1
> 24 1.00 285.12-239418.39 285.09 283.81 0.97 -1
> 25 1.00 279.17-239630.47 279.98 278.73 0.97 -1
> 26 1.00 276.92-239490.22 277.46 276.21 0.97 -1
> 27 -1.00 273.11-239656.31 273.71 273.71 0.90 -1
> 28 1.00 272.29-239793.97 272.47 271.23 0.77 -1
> 29 1.00 271.67-239750.30 271.23 272.47 0.90 -1
> 30 -1.00 273.12-239533.78 274.96 274.96 0.97 -1
> 31 -1.00 268.90-239618.69 270.00 270.00 0.65 -1
> 32 1.00 281.96-239330.79 281.25 282.53 1.03 -1
> # exchange 32
> 1 1.00 299.58-239343.43 299.52 298.19 0.94 -1
> 2 1.00 311.50-238980.95 310.44 309.01 0.06 -1
> 3 1.00 295.85-239184.29 296.86 295.53 1.00 -1
> 4 -1.00 308.17-239136.45 307.64 307.64 0.88 -1
> 5 1.00 308.06-238988.58 309.01 310.44 0.31 -1
> 6 1.00 305.13-239138.99 304.91 303.56 0.94 -1
> 7 1.00 297.85-239308.56 295.53 296.86 1.00 -1
> 8 1.00 301.01-239380.21 302.21 300.86 1.00 -1
> 9 1.00 298.53-239203.29 298.19 299.52 0.94 -1
> 10 -1.00 304.70-239232.45 306.27 306.27 0.88 -1
> 11 1.00 302.69-239202.78 303.56 304.91 1.00 -1
> 12 1.00 294.94-239499.66 294.21 292.90 1.00 -1
> 13 1.00 300.69-239395.23 300.86 302.21 0.94 -1
> 14 1.00 286.37-239695.11 286.38 285.09 1.00 -1
> 15 1.00 291.36-239520.08 290.28 291.58 1.00 -1
> 16 1.00 281.85-239685.86 281.25 279.98 1.00 -1
> 17 1.00 286.91-239521.64 287.68 288.97 1.00 -1
> 18 1.00 285.86-239469.74 285.09 286.38 1.00 -1
> 19 1.00 291.53-239557.96 291.58 290.28 0.94 -1
> 20 1.00 287.61-239612.47 288.97 287.68 1.00 -1
> 21 1.00 295.50-239511.96 292.90 294.21 1.00 -1
> 22 1.00 277.08-239728.20 277.46 278.73 1.00 -1
> 23 1.00 281.02-239549.47 279.98 281.25 1.00 -1
> 24 1.00 285.24-239811.81 283.81 282.53 1.00 -1
> 25 1.00 280.54-239919.66 278.73 277.46 1.00 -1
> 26 1.00 275.03-239906.59 276.21 274.96 1.00 -1
> 27 -1.00 273.96-239787.93 273.71 273.71 0.88 -1
> 28 1.00 271.41-239907.75 271.23 270.00 0.88 -1
> 29 -1.00 272.49-239881.87 272.47 272.47 0.75 -1
> 30 1.00 273.86-239793.13 274.96 276.21 1.00 -1
> 31 1.00 270.74-239929.02 270.00 271.23 0.69 -1
> 32 1.00 284.17-239559.23 282.53 283.81 1.00 -1
> # exchange 33
> 1 1.00 298.56-239647.71 298.19 296.86 0.91 -1
> 2 1.00 310.32-239222.61 309.01 307.64 0.30 -1
> 3 1.00 294.15-239565.38 295.53 294.21 0.97 -1
> 4 1.00 303.38-239211.71 307.64 309.01 0.91 -1
> 5 -1.00 311.39-239214.75 310.44 310.44 0.06 -1
> 6 1.00 303.15-239587.23 303.56 302.21 0.97 -1
> 7 1.00 295.82-239452.66 296.86 298.19 1.03 -1
> 8 1.00 301.75-239706.01 300.86 299.52 0.91 -1
> 9 1.00 299.23-239590.40 299.52 300.86 0.97 -1
> 10 1.00 306.48-239596.64 306.27 304.91 0.85 -1
> 11 1.00 304.11-239317.37 304.91 306.27 0.97 -1
> 12 1.00 295.12-239733.48 292.90 291.58 0.97 -1
> 13 1.00 302.37-239381.64 302.21 303.56 1.03 -1
> 14 1.00 285.43-239993.86 285.09 283.81 0.97 -1
> 15 1.00 293.03-239827.37 291.58 292.90 0.97 -1
> 16 1.00 281.71-240076.80 279.98 278.73 0.97 -1
> 17 1.00 287.46-239707.00 288.97 290.28 1.03 -1
> 18 1.00 287.92-239662.53 286.38 287.68 1.03 -1
> 19 1.00 289.38-239765.38 290.28 288.97 0.97 -1
> 20 1.00 287.47-239790.23 287.68 286.38 0.97 -1
> 21 1.00 293.81-239572.60 294.21 295.53 1.03 -1
> 22 1.00 279.07-239939.90 278.73 279.98 1.03 -1
> 23 1.00 279.45-239795.77 281.25 282.53 1.03 -1
> 24 1.00 282.05-240026.98 282.53 281.25 0.97 -1
> 25 1.00 280.62-240229.59 277.46 276.21 0.97 -1
> 26 1.00 276.37-240004.49 274.96 273.71 0.97 -1
> 27 1.00 274.39-240117.97 273.71 274.96 0.91 -1
> 28 -1.00 271.27-240176.99 270.00 270.00 0.67 -1
> 29 1.00 272.88-240227.77 272.47 271.23 0.73 -1
> 30 1.00 277.02-240107.91 276.21 277.46 1.03 -1
> 31 1.00 271.63-240007.57 271.23 272.47 0.91 -1
> 32 1.00 283.63-239721.84 283.81 285.09 1.03 -1
>
> Temperatures were selected using: http://folding.bmc.uu.se/remd/
> The temperatures are:
> 270.00, 271.24, 272.48, 273.73, 274.98, 276.24, 277.50, 278.76, 280.04,
> 281.31, 282.59, 283.87, 285.17, 286.46, 287.76, 289.06, 290.37, 291.68,
> 293.00, 294.32, 295.65, 296.98, 298.32, 299.66, 301.01, 302.35, 303.71,
> 305.07, 306.43, 307.81, 309.18, 310.57
>
> These temperatures are based on 102229 degrees of freedom for the system
> and a desired exchange probability of .22. According to my mdout files,
> the system actually has 101423 degrees of freedom. So I think the
> temperatures may be a bit off, but I would be very surprised if they were
> responsible for anything as drastically weird as what I'm seeing.
>
> Has anybody seen these types of results before? What was the the cause?
> How did yo solve it?
>
> Christopher Thiebaut
> Graduate Student
> Purdue University
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
------------------------------
Message: 3
Date: Mon, 7 Apr 2014 16:02:28 -0400 (EDT)
From: Christopher A Thiebaut <cthieba.purdue.edu>
Subject: Re: [AMBER] Really Weird Problem with Replica Exchange
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<981849905.88714.1396900948772.JavaMail.root.mailhub055.itcs.purdue.edu>
Content-Type: text/plain; charset=utf-8
The initial structure was thermolysin with no ligand bound (will be doing simulations with a variety of ligands bound later on) solvated in a TIP3P truncated octahedron with periodic boundary conditions. I minimized the solvent with the protein restrained, then minimized the system as a whole, did a brief NVT simulation to get my system up to a reasonabe temperature, which was in the middle of my range. Then I did a short NPT simulation (at the same temperature, 1 atm pressure) to correct the density. Technically, I know that density won't be quite right at most of my temperatures but I don't have a huge temperature range so I don't think it should really be troublingly off either. Then I did 32 separate equilibrations based on that structure (at the replica exchange temperatures) before finally moving to the replica exchange simulation.
Christopher Thiebaut
Graduate Student
Purdue University
----- Original Message -----
From: "Carlos Simmerling" <carlos.simmerling.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Monday, April 7, 2014 3:48:18 PM
Subject: Re: [AMBER] Really Weird Problem with Replica Exchange
what were the initial structures? were they pre-equilibrated that the right
Ts? tell us more about how you got to this point...
On Mon, Apr 7, 2014 at 2:58 PM, Christopher A Thiebaut
<cthieba.purdue.edu>wrote:
> Helllo all,
>
> I am having what I imagine to be a very unusual problem running replica
> exchange of thermolysin solvated with explicit TIP3P water.
> The simulations will run without any error messages, but I am sure the
> results I am seeing are not meaningful because most replicas are exchanging
> at most exchange attempts and even more so because the volocity scaling is
> always 1.0 (meaning the volocites are not changed at all), except once
> during the first exchange. In addition, the total potential energy seems
> to be slowly increasing throughout the simulation which also should not be
> happening.
>
> Here's a sample of my rem.log file so you can see what I'm talking about:
> # Rep#, Velocity Scaling, T, Eptot, Temp0, NewTemp0, Success rate (i,i+1),
> ResStruct#
> # exchange 1
> 1 1.07 0.00-158275.28 270.00 310.44 0.00 -1
> 2 1.00 0.00-158841.35 271.23 272.47 2.00 -1
> 3 1.00 0.00-159708.30 272.47 271.23 0.00 -1
> 4 1.00 0.00-159547.14 273.71 274.96 2.00 -1
> 5 1.00 0.00-159457.82 274.96 273.71 0.00 -1
> 6 1.00 0.00-160730.25 276.21 277.46 2.00 -1
> 7 1.00 0.00-160858.37 277.46 276.21 0.00 -1
> 8 1.00 0.00-161155.52 278.73 279.98 2.00 -1
> 9 1.00 0.00-161044.87 279.98 278.73 0.00 -1
> 10 1.00 0.00-161039.89 281.25 282.53 2.00 -1
> 11 1.00 0.00-161096.24 282.53 281.25 0.00 -1
> 12 1.00 0.00-162494.74 283.81 285.09 2.00 -1
> 13 1.00 0.00-162767.85 285.09 283.81 0.00 -1
> 14 1.00 0.00-161902.49 286.38 287.68 2.00 -1
> 15 1.00 0.00-163145.99 287.68 286.38 0.00 -1
> 16 1.00 0.00-162901.03 288.97 290.28 2.00 -1
> 17 1.00 0.00-164106.69 290.28 288.97 0.00 -1
> 18 -1.00 0.00-163819.64 291.58 291.58 0.00 -1
> 19 -1.00 0.00-163549.67 292.90 292.90 0.00 -1
> 20 1.00 0.00-163950.79 294.21 295.53 2.00 -1
> 21 1.00 0.00-164690.76 295.53 294.21 0.00 -1
> 22 1.00 0.00-165187.80 296.86 298.19 2.00 -1
> 23 1.00 0.00-165377.17 298.19 296.86 0.00 -1
> 24 -1.00 0.00-164848.36 299.52 299.52 0.00 -1
> 25 -1.00 0.00-164797.83 300.86 300.86 0.00 -1
> 26 1.00 0.00-165237.92 302.21 303.56 2.00 -1
> 27 1.00 0.00-166216.65 303.56 302.21 0.00 -1
> 28 1.00 0.00-166127.19 304.91 306.27 2.00 -1
> 29 1.00 0.00-167327.09 306.27 304.91 0.00 -1
> 30 1.00 0.00-166545.00 307.64 309.01 2.00 -1
> 31 1.00 0.00-168071.75 309.01 307.64 0.00 -1
> 32 0.93 0.00-167178.34 310.44 270.00 2.00 -1
> ......................................................................
> # exchange 25
> 1 1.00 309.91-237311.34 309.01 307.64 0.08 -1
> 2 1.00 304.26-237005.16 302.21 303.56 1.04 -1
> 3 1.00 296.00-237356.49 296.86 298.19 1.04 -1
> 4 1.00 304.33-237213.57 304.91 306.27 0.96 -1
> 5 1.00 300.61-237074.41 299.52 300.86 0.96 -1
> 6 1.00 306.71-237010.94 307.64 309.01 0.88 -1
> 7 1.00 288.23-237533.96 286.38 287.68 1.04 -1
> 8 -1.00 309.85-237252.49 310.44 310.44 0.08 -1
> 9 1.00 289.99-237569.69 288.97 290.28 1.04 -1
> 10 1.00 307.03-237289.10 306.27 304.91 0.88 -1
> 11 1.00 296.78-237439.24 294.21 295.53 1.04 -1
> 12 1.00 302.80-237548.07 303.56 302.21 0.96 -1
> 13 1.00 291.19-237476.28 291.58 292.90 0.96 -1
> 14 1.00 298.13-237536.76 295.53 294.21 0.96 -1
> 15 1.00 284.22-237758.43 281.25 282.53 1.04 -1
> 16 1.00 291.28-237590.61 290.28 288.97 0.96 -1
> 17 1.00 277.07-237711.31 278.73 279.98 1.04 -1
> 18 1.00 277.52-237747.34 276.21 277.46 1.04 -1
> 19 1.00 300.95-237501.70 300.86 299.52 0.96 -1
> 20 1.00 297.03-237561.12 298.19 296.86 0.88 -1
> 21 1.00 282.63-237651.93 283.81 285.09 1.04 -1
> 22 -1.00 270.53-238135.36 270.00 270.00 0.56 -1
> 23 1.00 272.50-237928.60 271.23 272.47 0.88 -1
> 24 1.00 292.11-237641.94 292.90 291.58 0.96 -1
> 25 1.00 288.51-237686.39 287.68 286.38 0.96 -1
> 26 1.00 285.15-237838.02 285.09 283.81 0.96 -1
> 27 1.00 269.94-237998.93 272.47 271.23 0.72 -1
> 28 1.00 278.70-237910.14 279.98 278.73 0.96 -1
> 29 1.00 275.61-238021.61 274.96 273.71 0.96 -1
> 30 1.00 282.57-237916.92 282.53 281.25 0.96 -1
> 31 1.00 276.88-238031.26 277.46 276.21 0.96 -1
> 32 1.00 273.65-237788.60 273.71 274.96 0.96 -1
> # exchange 26
> 1 1.00 309.43-237528.66 307.64 306.27 0.85 -1
> 2 1.00 303.95-237551.08 303.56 304.91 1.00 -1
> 3 1.00 297.95-237809.91 298.19 299.52 0.92 -1
> 4 1.00 306.31-237657.13 306.27 307.64 0.92 -1
> 5 1.00 299.96-237577.66 300.86 302.21 1.00 -1
> 6 1.00 308.95-237472.73 309.01 310.44 0.15 -1
> 7 1.00 286.56-237844.08 287.68 288.97 1.00 -1
> 8 1.00 310.00-237519.31 310.44 309.01 0.08 -1
> 9 1.00 291.81-237729.64 290.28 291.58 1.00 -1
> 10 1.00 303.70-237715.75 304.91 303.56 0.92 -1
> 11 1.00 296.62-237700.83 295.53 296.86 1.00 -1
> 12 1.00 303.16-237772.77 302.21 300.86 1.00 -1
> 13 1.00 292.60-237770.36 292.90 294.21 1.00 -1
> 14 1.00 293.41-237816.24 294.21 292.90 1.00 -1
> 15 1.00 282.61-237999.04 282.53 283.81 1.00 -1
> 16 1.00 289.23-237958.84 288.97 287.68 1.00 -1
> 17 1.00 278.69-238016.41 279.98 281.25 1.00 -1
> 18 1.00 278.70-238051.34 277.46 278.73 1.00 -1
> 19 1.00 298.26-237923.06 299.52 298.19 0.92 -1
> 20 1.00 293.43-237819.98 296.86 295.53 1.00 -1
> 21 1.00 285.90-237872.36 285.09 286.38 1.00 -1
> 22 1.00 271.15-238192.37 270.00 271.23 0.62 -1
> 23 1.00 272.53-238207.17 272.47 273.71 0.77 -1
> 24 1.00 290.92-238028.52 291.58 290.28 0.92 -1
> 25 1.00 286.71-238159.73 286.38 285.09 1.00 -1
> 26 1.00 284.16-238189.10 283.81 282.53 1.00 -1
> 27 1.00 272.89-238264.83 271.23 270.00 0.85 -1
> 28 1.00 278.46-238289.12 278.73 277.46 1.00 -1
> 29 1.00 272.73-238268.68 273.71 272.47 0.92 -1
> 30 1.00 281.90-238206.67 281.25 279.98 1.00 -1
> 31 1.00 279.16-238218.60 276.21 274.96 1.00 -1
> 32 1.00 273.42-238084.44 274.96 276.21 1.00 -1
> # exchange 27
> 1 1.00 305.14-237896.37 306.27 304.91 0.89 -1
> 2 1.00 306.70-237688.11 304.91 306.27 0.96 -1
> 3 1.00 299.55-237906.46 299.52 300.86 0.96 -1
> 4 1.00 308.78-237779.85 307.64 309.01 0.89 -1
> 5 1.00 303.02-237740.95 302.21 303.56 1.04 -1
> 6 -1.00 312.04-237760.32 310.44 310.44 0.07 -1
> 7 1.00 289.44-238148.68 288.97 290.28 1.04 -1
> 8 1.00 308.40-237883.47 309.01 307.64 0.15 -1
> 9 1.00 293.62-238039.32 291.58 292.90 0.96 -1
> 10 1.00 303.22-237972.21 303.56 302.21 0.96 -1
> 11 1.00 298.26-238017.06 296.86 298.19 1.04 -1
> 12 1.00 302.52-238053.44 300.86 299.52 0.96 -1
> 13 1.00 297.91-238061.27 294.21 295.53 1.04 -1
> 14 1.00 293.39-238165.74 292.90 291.58 0.96 -1
> 15 1.00 286.69-238367.18 283.81 285.09 1.04 -1
> 16 1.00 285.33-238372.24 287.68 286.38 0.96 -1
> 17 1.00 280.09-238415.47 281.25 282.53 1.04 -1
> 18 1.00 279.14-238456.86 278.73 279.98 1.04 -1
> 19 1.00 297.69-238179.86 298.19 296.86 0.89 -1
> 20 1.00 293.78-238363.05 295.53 294.21 0.96 -1
> 21 1.00 286.04-238315.32 286.38 287.68 1.04 -1
> 22 1.00 269.92-238495.65 271.23 272.47 0.89 -1
> 23 1.00 272.51-238431.54 273.71 274.96 0.96 -1
> 24 1.00 289.51-238323.64 290.28 288.97 0.96 -1
> 25 1.00 285.80-238400.25 285.09 283.81 0.96 -1
> 26 1.00 284.11-238504.05 282.53 281.25 0.96 -1
> 27 -1.00 270.33-238639.41 270.00 270.00 0.59 -1
> 28 1.00 278.26-238633.26 277.46 276.21 0.96 -1
> 29 1.00 271.87-238758.14 272.47 271.23 0.74 -1
> 30 1.00 278.97-238406.37 279.98 278.73 0.96 -1
> 31 1.00 275.36-238642.13 274.96 273.71 0.96 -1
> 32 1.00 277.11-238336.79 276.21 277.46 1.04 -1
> # exchange 28
> 1 1.00 305.41-238178.28 304.91 303.56 0.93 -1
> 2 1.00 308.72-237888.75 306.27 307.64 0.93 -1
> 3 -1.00 299.85-238411.98 300.86 300.86 0.93 -1
> 4 1.00 308.47-237966.66 309.01 310.44 0.21 -1
> 5 1.00 302.86-237989.18 303.56 304.91 1.00 -1
> 6 1.00 310.64-238126.41 310.44 309.01 0.07 -1
> 7 1.00 291.09-238323.96 290.28 291.58 1.00 -1
> 8 1.00 306.54-238287.31 307.64 306.27 0.86 -1
> 9 1.00 292.28-238398.82 292.90 294.21 1.00 -1
> 10 -1.00 302.07-238374.29 302.21 302.21 1.00 -1
> 11 1.00 299.33-238367.94 298.19 299.52 0.93 -1
> 12 1.00 299.74-238329.33 299.52 298.19 0.93 -1
> 13 1.00 294.48-238329.94 295.53 296.86 1.00 -1
> 14 1.00 292.88-238512.89 291.58 290.28 0.93 -1
> 15 1.00 284.54-238592.77 285.09 286.38 1.00 -1
> 16 1.00 289.06-238586.60 286.38 285.09 1.00 -1
> 17 1.00 282.18-238604.33 282.53 283.81 1.00 -1
> 18 1.00 280.42-238498.62 279.98 281.25 1.00 -1
> 19 1.00 298.42-238339.10 296.86 295.53 1.00 -1
> 20 1.00 295.23-238501.82 294.21 292.90 1.00 -1
> 21 1.00 287.96-238622.69 287.68 288.97 1.00 -1
> 22 1.00 274.59-238791.23 272.47 273.71 0.79 -1
> 23 1.00 274.34-238732.39 274.96 276.21 1.00 -1
> 24 1.00 290.89-238503.91 288.97 287.68 1.00 -1
> 25 1.00 284.40-238719.97 283.81 282.53 1.00 -1
> 26 1.00 281.12-238697.12 281.25 279.98 1.00 -1
> 27 1.00 271.44-238981.93 270.00 271.23 0.64 -1
> 28 1.00 277.56-238877.61 276.21 274.96 1.00 -1
> 29 1.00 272.58-239072.51 271.23 270.00 0.86 -1
> 30 1.00 279.19-238902.86 278.73 277.46 1.00 -1
> 31 1.00 274.58-238952.80 273.71 272.47 0.93 -1
> 32 1.00 278.29-238672.97 277.46 278.73 1.00 -1
> # exchange 29
> 1 1.00 303.10-238482.53 303.56 302.21 0.97 -1
> 2 1.00 308.47-238268.33 307.64 309.01 0.90 -1
> 3 1.00 300.90-238576.50 300.86 299.52 0.90 -1
> 4 -1.00 310.92-238315.71 310.44 310.44 0.07 -1
> 5 1.00 304.45-238317.36 304.91 306.27 0.97 -1
> 6 1.00 307.80-238499.68 309.01 307.64 0.21 -1
> 7 1.00 291.95-238596.78 291.58 292.90 0.97 -1
> 8 1.00 306.74-238454.39 306.27 304.91 0.90 -1
> 9 1.00 294.77-238569.62 294.21 295.53 1.03 -1
> 10 1.00 303.24-238531.15 302.21 303.56 1.03 -1
> 11 1.00 299.01-238638.43 299.52 300.86 0.97 -1
> 12 1.00 299.36-238835.63 298.19 296.86 0.90 -1
> 13 1.00 298.09-238588.55 296.86 298.19 1.03 -1
> 14 1.00 291.63-238777.70 290.28 288.97 0.97 -1
> 15 1.00 286.85-239032.37 286.38 287.68 1.03 -1
> 16 1.00 285.69-238846.49 285.09 283.81 0.97 -1
> 17 1.00 282.94-238892.18 283.81 285.09 1.03 -1
> 18 1.00 281.44-238894.57 281.25 282.53 1.03 -1
> 19 1.00 296.81-238719.29 295.53 294.21 0.97 -1
> 20 1.00 293.05-238860.89 292.90 291.58 0.97 -1
> 21 1.00 286.63-238769.89 288.97 290.28 1.03 -1
> 22 1.00 276.10-238983.43 273.71 274.96 0.97 -1
> 23 1.00 278.03-238930.08 276.21 277.46 1.03 -1
> 24 1.00 286.91-238958.25 287.68 286.38 0.97 -1
> 25 1.00 282.26-239046.26 282.53 281.25 0.97 -1
> 26 1.00 279.78-239123.91 279.98 278.73 0.97 -1
> 27 1.00 273.78-239151.24 271.23 272.47 0.90 -1
> 28 1.00 275.98-239171.49 274.96 273.71 0.97 -1
> 29 -1.00 269.99-239317.35 270.00 270.00 0.62 -1
> 30 1.00 276.91-239191.40 277.46 276.21 0.97 -1
> 31 1.00 272.73-239255.54 272.47 271.23 0.76 -1
> 32 1.00 279.96-238888.03 278.73 279.98 1.03 -1
> # exchange 30
> 1 1.00 302.64-238842.01 302.21 300.86 1.00 -1
> 2 1.00 308.63-238427.17 309.01 310.44 0.27 -1
> 3 1.00 299.84-238911.95 299.52 298.19 0.93 -1
> 4 1.00 309.86-238515.73 310.44 309.01 0.07 -1
> 5 1.00 307.42-238560.64 306.27 307.64 0.93 -1
> 6 1.00 307.48-238702.43 307.64 306.27 0.87 -1
> 7 1.00 292.53-238839.87 292.90 294.21 1.00 -1
> 8 1.00 306.00-238777.41 304.91 303.56 0.93 -1
> 9 1.00 297.32-238947.72 295.53 296.86 1.00 -1
> 10 1.00 304.05-238883.82 303.56 304.91 1.00 -1
> 11 1.00 302.57-238780.54 300.86 302.21 0.93 -1
> 12 1.00 292.21-238910.66 296.86 295.53 1.00 -1
> 13 1.00 298.97-238780.23 298.19 299.52 0.93 -1
> 14 1.00 286.86-239171.01 288.97 287.68 1.00 -1
> 15 1.00 290.28-239150.80 287.68 288.97 1.00 -1
> 16 1.00 282.76-239323.47 283.81 282.53 1.00 -1
> 17 1.00 284.27-239063.46 285.09 286.38 1.00 -1
> 18 1.00 281.82-239049.67 282.53 283.81 1.00 -1
> 19 1.00 292.78-239024.98 294.21 292.90 1.00 -1
> 20 1.00 293.24-239149.18 291.58 290.28 0.93 -1
> 21 1.00 291.56-239013.66 290.28 291.58 1.00 -1
> 22 1.00 276.39-239397.26 274.96 276.21 1.00 -1
> 23 1.00 278.04-239172.39 277.46 278.73 1.00 -1
> 24 1.00 287.81-239189.88 286.38 285.09 1.00 -1
> 25 1.00 281.80-239499.51 281.25 279.98 1.00 -1
> 26 1.00 279.53-239167.74 278.73 277.46 1.00 -1
> 27 1.00 272.13-239418.19 272.47 273.71 0.80 -1
> 28 1.00 273.73-239459.18 273.71 272.47 0.93 -1
> 29 1.00 269.25-239534.80 270.00 271.23 0.67 -1
> 30 1.00 278.19-239456.51 276.21 274.96 1.00 -1
> 31 1.00 267.89-239471.35 271.23 270.00 0.87 -1
> 32 1.00 282.43-239161.13 279.98 281.25 1.00 -1
> # exchange 31
> 1 1.00 301.00-238974.09 300.86 299.52 0.90 -1
> 2 -1.00 309.61-238660.96 310.44 310.44 0.06 -1
> 3 1.00 299.18-239060.07 298.19 296.86 0.90 -1
> 4 1.00 310.05-238867.09 309.01 307.64 0.26 -1
> 5 1.00 305.97-238751.83 307.64 309.01 0.90 -1
> 6 1.00 303.80-238862.17 306.27 304.91 0.90 -1
> 7 1.00 294.92-239133.23 294.21 295.53 1.03 -1
> 8 1.00 300.79-239134.89 303.56 302.21 0.97 -1
> 9 1.00 295.27-239078.59 296.86 298.19 1.03 -1
> 10 1.00 307.38-238976.05 304.91 306.27 0.97 -1
> 11 1.00 299.93-239007.75 302.21 303.56 1.03 -1
> 12 1.00 296.23-239266.13 295.53 294.21 0.97 -1
> 13 1.00 300.31-238964.11 299.52 300.86 0.97 -1
> 14 1.00 288.87-239491.68 287.68 286.38 0.97 -1
> 15 1.00 288.87-239181.78 288.97 290.28 1.03 -1
> 16 1.00 283.85-239447.44 282.53 281.25 0.97 -1
> 17 1.00 286.93-239387.00 286.38 287.68 1.03 -1
> 18 1.00 285.28-239293.13 283.81 285.09 1.03 -1
> 19 1.00 294.38-239262.60 292.90 291.58 0.97 -1
> 20 1.00 291.41-239473.95 290.28 288.97 0.97 -1
> 21 1.00 291.99-239025.10 291.58 292.90 0.97 -1
> 22 1.00 277.99-239464.65 276.21 277.46 1.03 -1
> 23 1.00 280.21-239389.24 278.73 279.98 1.03 -1
> 24 1.00 285.12-239418.39 285.09 283.81 0.97 -1
> 25 1.00 279.17-239630.47 279.98 278.73 0.97 -1
> 26 1.00 276.92-239490.22 277.46 276.21 0.97 -1
> 27 -1.00 273.11-239656.31 273.71 273.71 0.90 -1
> 28 1.00 272.29-239793.97 272.47 271.23 0.77 -1
> 29 1.00 271.67-239750.30 271.23 272.47 0.90 -1
> 30 -1.00 273.12-239533.78 274.96 274.96 0.97 -1
> 31 -1.00 268.90-239618.69 270.00 270.00 0.65 -1
> 32 1.00 281.96-239330.79 281.25 282.53 1.03 -1
> # exchange 32
> 1 1.00 299.58-239343.43 299.52 298.19 0.94 -1
> 2 1.00 311.50-238980.95 310.44 309.01 0.06 -1
> 3 1.00 295.85-239184.29 296.86 295.53 1.00 -1
> 4 -1.00 308.17-239136.45 307.64 307.64 0.88 -1
> 5 1.00 308.06-238988.58 309.01 310.44 0.31 -1
> 6 1.00 305.13-239138.99 304.91 303.56 0.94 -1
> 7 1.00 297.85-239308.56 295.53 296.86 1.00 -1
> 8 1.00 301.01-239380.21 302.21 300.86 1.00 -1
> 9 1.00 298.53-239203.29 298.19 299.52 0.94 -1
> 10 -1.00 304.70-239232.45 306.27 306.27 0.88 -1
> 11 1.00 302.69-239202.78 303.56 304.91 1.00 -1
> 12 1.00 294.94-239499.66 294.21 292.90 1.00 -1
> 13 1.00 300.69-239395.23 300.86 302.21 0.94 -1
> 14 1.00 286.37-239695.11 286.38 285.09 1.00 -1
> 15 1.00 291.36-239520.08 290.28 291.58 1.00 -1
> 16 1.00 281.85-239685.86 281.25 279.98 1.00 -1
> 17 1.00 286.91-239521.64 287.68 288.97 1.00 -1
> 18 1.00 285.86-239469.74 285.09 286.38 1.00 -1
> 19 1.00 291.53-239557.96 291.58 290.28 0.94 -1
> 20 1.00 287.61-239612.47 288.97 287.68 1.00 -1
> 21 1.00 295.50-239511.96 292.90 294.21 1.00 -1
> 22 1.00 277.08-239728.20 277.46 278.73 1.00 -1
> 23 1.00 281.02-239549.47 279.98 281.25 1.00 -1
> 24 1.00 285.24-239811.81 283.81 282.53 1.00 -1
> 25 1.00 280.54-239919.66 278.73 277.46 1.00 -1
> 26 1.00 275.03-239906.59 276.21 274.96 1.00 -1
> 27 -1.00 273.96-239787.93 273.71 273.71 0.88 -1
> 28 1.00 271.41-239907.75 271.23 270.00 0.88 -1
> 29 -1.00 272.49-239881.87 272.47 272.47 0.75 -1
> 30 1.00 273.86-239793.13 274.96 276.21 1.00 -1
> 31 1.00 270.74-239929.02 270.00 271.23 0.69 -1
> 32 1.00 284.17-239559.23 282.53 283.81 1.00 -1
> # exchange 33
> 1 1.00 298.56-239647.71 298.19 296.86 0.91 -1
> 2 1.00 310.32-239222.61 309.01 307.64 0.30 -1
> 3 1.00 294.15-239565.38 295.53 294.21 0.97 -1
> 4 1.00 303.38-239211.71 307.64 309.01 0.91 -1
> 5 -1.00 311.39-239214.75 310.44 310.44 0.06 -1
> 6 1.00 303.15-239587.23 303.56 302.21 0.97 -1
> 7 1.00 295.82-239452.66 296.86 298.19 1.03 -1
> 8 1.00 301.75-239706.01 300.86 299.52 0.91 -1
> 9 1.00 299.23-239590.40 299.52 300.86 0.97 -1
> 10 1.00 306.48-239596.64 306.27 304.91 0.85 -1
> 11 1.00 304.11-239317.37 304.91 306.27 0.97 -1
> 12 1.00 295.12-239733.48 292.90 291.58 0.97 -1
> 13 1.00 302.37-239381.64 302.21 303.56 1.03 -1
> 14 1.00 285.43-239993.86 285.09 283.81 0.97 -1
> 15 1.00 293.03-239827.37 291.58 292.90 0.97 -1
> 16 1.00 281.71-240076.80 279.98 278.73 0.97 -1
> 17 1.00 287.46-239707.00 288.97 290.28 1.03 -1
> 18 1.00 287.92-239662.53 286.38 287.68 1.03 -1
> 19 1.00 289.38-239765.38 290.28 288.97 0.97 -1
> 20 1.00 287.47-239790.23 287.68 286.38 0.97 -1
> 21 1.00 293.81-239572.60 294.21 295.53 1.03 -1
> 22 1.00 279.07-239939.90 278.73 279.98 1.03 -1
> 23 1.00 279.45-239795.77 281.25 282.53 1.03 -1
> 24 1.00 282.05-240026.98 282.53 281.25 0.97 -1
> 25 1.00 280.62-240229.59 277.46 276.21 0.97 -1
> 26 1.00 276.37-240004.49 274.96 273.71 0.97 -1
> 27 1.00 274.39-240117.97 273.71 274.96 0.91 -1
> 28 -1.00 271.27-240176.99 270.00 270.00 0.67 -1
> 29 1.00 272.88-240227.77 272.47 271.23 0.73 -1
> 30 1.00 277.02-240107.91 276.21 277.46 1.03 -1
> 31 1.00 271.63-240007.57 271.23 272.47 0.91 -1
> 32 1.00 283.63-239721.84 283.81 285.09 1.03 -1
>
> Temperatures were selected using: http://folding.bmc.uu.se/remd/
> The temperatures are:
> 270.00, 271.24, 272.48, 273.73, 274.98, 276.24, 277.50, 278.76, 280.04,
> 281.31, 282.59, 283.87, 285.17, 286.46, 287.76, 289.06, 290.37, 291.68,
> 293.00, 294.32, 295.65, 296.98, 298.32, 299.66, 301.01, 302.35, 303.71,
> 305.07, 306.43, 307.81, 309.18, 310.57
>
> These temperatures are based on 102229 degrees of freedom for the system
> and a desired exchange probability of .22. According to my mdout files,
> the system actually has 101423 degrees of freedom. So I think the
> temperatures may be a bit off, but I would be very surprised if they were
> responsible for anything as drastically weird as what I'm seeing.
>
> Has anybody seen these types of results before? What was the the cause?
> How did yo solve it?
>
> Christopher Thiebaut
> Graduate Student
> Purdue University
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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------------------------------
Message: 4
Date: Mon, 7 Apr 2014 14:08:28 -0600
From: Christina Bergonzo <cbergonzo.gmail.com>
Subject: Re: [AMBER] Really Weird Problem with Replica Exchange
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAMLwDJ1Ri+Sx6J7onSkDLS29VSwKmPKJKiUdvy_3qQP83+hfMg.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi Christopher,
Even if you have independently equilibrated the starting structures, it can
take a while for the exchange probability to average out. This is system
size dependent, and could take much longer than 30-ish exchanges. The
exchange probability should start out at 0, though, and rise to whatever
acceptance % you set up. The high initial acceptance tells me these
replicas may be set up too closely, though I have used the same temperature
generator before and gotten a good distribution out of it.
In addition to what Carlos asked, how many atoms/how many water molecules
are in your system? And what are you trying to sample here? A high
temperature of ~300K seems too low to enhance sampling all that much. The
T-REMD tutorial suggests using a range potentially up to 600K:
http://ambermd.org/tutorials/advanced/tutorial7/
-Christina
On Mon, Apr 7, 2014 at 2:02 PM, Christopher A Thiebaut
<cthieba.purdue.edu>wrote:
> The initial structure was thermolysin with no ligand bound (will be doing
> simulations with a variety of ligands bound later on) solvated in a TIP3P
> truncated octahedron with periodic boundary conditions. I minimized the
> solvent with the protein restrained, then minimized the system as a whole,
> did a brief NVT simulation to get my system up to a reasonabe temperature,
> which was in the middle of my range. Then I did a short NPT simulation (at
> the same temperature, 1 atm pressure) to correct the density. Technically,
> I know that density won't be quite right at most of my temperatures but I
> don't have a huge temperature range so I don't think it should really be
> troublingly off either. Then I did 32 separate equilibrations based on that
> structure (at the replica exchange temperatures) before finally moving to
> the replica exchange simulation.
>
> Christopher Thiebaut
> Graduate Student
> Purdue University
> ----- Original Message -----
> From: "Carlos Simmerling" <carlos.simmerling.gmail.com>
> To: "AMBER Mailing List" <amber.ambermd.org>
> Sent: Monday, April 7, 2014 3:48:18 PM
> Subject: Re: [AMBER] Really Weird Problem with Replica Exchange
>
> what were the initial structures? were they pre-equilibrated that the right
> Ts? tell us more about how you got to this point...
>
>
> On Mon, Apr 7, 2014 at 2:58 PM, Christopher A Thiebaut
> <cthieba.purdue.edu>wrote:
>
> > Helllo all,
> >
> > I am having what I imagine to be a very unusual problem running replica
> > exchange of thermolysin solvated with explicit TIP3P water.
> > The simulations will run without any error messages, but I am sure the
> > results I am seeing are not meaningful because most replicas are
> exchanging
> > at most exchange attempts and even more so because the volocity scaling
> is
> > always 1.0 (meaning the volocites are not changed at all), except once
> > during the first exchange. In addition, the total potential energy seems
> > to be slowly increasing throughout the simulation which also should not
> be
> > happening.
> >
> > Here's a sample of my rem.log file so you can see what I'm talking about:
> > # Rep#, Velocity Scaling, T, Eptot, Temp0, NewTemp0, Success rate
> (i,i+1),
> > ResStruct#
> > # exchange 1
> > 1 1.07 0.00-158275.28 270.00 310.44 0.00 -1
> > 2 1.00 0.00-158841.35 271.23 272.47 2.00 -1
> > 3 1.00 0.00-159708.30 272.47 271.23 0.00 -1
> > 4 1.00 0.00-159547.14 273.71 274.96 2.00 -1
> > 5 1.00 0.00-159457.82 274.96 273.71 0.00 -1
> > 6 1.00 0.00-160730.25 276.21 277.46 2.00 -1
> > 7 1.00 0.00-160858.37 277.46 276.21 0.00 -1
> > 8 1.00 0.00-161155.52 278.73 279.98 2.00 -1
> > 9 1.00 0.00-161044.87 279.98 278.73 0.00 -1
> > 10 1.00 0.00-161039.89 281.25 282.53 2.00 -1
> > 11 1.00 0.00-161096.24 282.53 281.25 0.00 -1
> > 12 1.00 0.00-162494.74 283.81 285.09 2.00 -1
> > 13 1.00 0.00-162767.85 285.09 283.81 0.00 -1
> > 14 1.00 0.00-161902.49 286.38 287.68 2.00 -1
> > 15 1.00 0.00-163145.99 287.68 286.38 0.00 -1
> > 16 1.00 0.00-162901.03 288.97 290.28 2.00 -1
> > 17 1.00 0.00-164106.69 290.28 288.97 0.00 -1
> > 18 -1.00 0.00-163819.64 291.58 291.58 0.00 -1
> > 19 -1.00 0.00-163549.67 292.90 292.90 0.00 -1
> > 20 1.00 0.00-163950.79 294.21 295.53 2.00 -1
> > 21 1.00 0.00-164690.76 295.53 294.21 0.00 -1
> > 22 1.00 0.00-165187.80 296.86 298.19 2.00 -1
> > 23 1.00 0.00-165377.17 298.19 296.86 0.00 -1
> > 24 -1.00 0.00-164848.36 299.52 299.52 0.00 -1
> > 25 -1.00 0.00-164797.83 300.86 300.86 0.00 -1
> > 26 1.00 0.00-165237.92 302.21 303.56 2.00 -1
> > 27 1.00 0.00-166216.65 303.56 302.21 0.00 -1
> > 28 1.00 0.00-166127.19 304.91 306.27 2.00 -1
> > 29 1.00 0.00-167327.09 306.27 304.91 0.00 -1
> > 30 1.00 0.00-166545.00 307.64 309.01 2.00 -1
> > 31 1.00 0.00-168071.75 309.01 307.64 0.00 -1
> > 32 0.93 0.00-167178.34 310.44 270.00 2.00 -1
> > ......................................................................
> > # exchange 25
> > 1 1.00 309.91-237311.34 309.01 307.64 0.08 -1
> > 2 1.00 304.26-237005.16 302.21 303.56 1.04 -1
> > 3 1.00 296.00-237356.49 296.86 298.19 1.04 -1
> > 4 1.00 304.33-237213.57 304.91 306.27 0.96 -1
> > 5 1.00 300.61-237074.41 299.52 300.86 0.96 -1
> > 6 1.00 306.71-237010.94 307.64 309.01 0.88 -1
> > 7 1.00 288.23-237533.96 286.38 287.68 1.04 -1
> > 8 -1.00 309.85-237252.49 310.44 310.44 0.08 -1
> > 9 1.00 289.99-237569.69 288.97 290.28 1.04 -1
> > 10 1.00 307.03-237289.10 306.27 304.91 0.88 -1
> > 11 1.00 296.78-237439.24 294.21 295.53 1.04 -1
> > 12 1.00 302.80-237548.07 303.56 302.21 0.96 -1
> > 13 1.00 291.19-237476.28 291.58 292.90 0.96 -1
> > 14 1.00 298.13-237536.76 295.53 294.21 0.96 -1
> > 15 1.00 284.22-237758.43 281.25 282.53 1.04 -1
> > 16 1.00 291.28-237590.61 290.28 288.97 0.96 -1
> > 17 1.00 277.07-237711.31 278.73 279.98 1.04 -1
> > 18 1.00 277.52-237747.34 276.21 277.46 1.04 -1
> > 19 1.00 300.95-237501.70 300.86 299.52 0.96 -1
> > 20 1.00 297.03-237561.12 298.19 296.86 0.88 -1
> > 21 1.00 282.63-237651.93 283.81 285.09 1.04 -1
> > 22 -1.00 270.53-238135.36 270.00 270.00 0.56 -1
> > 23 1.00 272.50-237928.60 271.23 272.47 0.88 -1
> > 24 1.00 292.11-237641.94 292.90 291.58 0.96 -1
> > 25 1.00 288.51-237686.39 287.68 286.38 0.96 -1
> > 26 1.00 285.15-237838.02 285.09 283.81 0.96 -1
> > 27 1.00 269.94-237998.93 272.47 271.23 0.72 -1
> > 28 1.00 278.70-237910.14 279.98 278.73 0.96 -1
> > 29 1.00 275.61-238021.61 274.96 273.71 0.96 -1
> > 30 1.00 282.57-237916.92 282.53 281.25 0.96 -1
> > 31 1.00 276.88-238031.26 277.46 276.21 0.96 -1
> > 32 1.00 273.65-237788.60 273.71 274.96 0.96 -1
> > # exchange 26
> > 1 1.00 309.43-237528.66 307.64 306.27 0.85 -1
> > 2 1.00 303.95-237551.08 303.56 304.91 1.00 -1
> > 3 1.00 297.95-237809.91 298.19 299.52 0.92 -1
> > 4 1.00 306.31-237657.13 306.27 307.64 0.92 -1
> > 5 1.00 299.96-237577.66 300.86 302.21 1.00 -1
> > 6 1.00 308.95-237472.73 309.01 310.44 0.15 -1
> > 7 1.00 286.56-237844.08 287.68 288.97 1.00 -1
> > 8 1.00 310.00-237519.31 310.44 309.01 0.08 -1
> > 9 1.00 291.81-237729.64 290.28 291.58 1.00 -1
> > 10 1.00 303.70-237715.75 304.91 303.56 0.92 -1
> > 11 1.00 296.62-237700.83 295.53 296.86 1.00 -1
> > 12 1.00 303.16-237772.77 302.21 300.86 1.00 -1
> > 13 1.00 292.60-237770.36 292.90 294.21 1.00 -1
> > 14 1.00 293.41-237816.24 294.21 292.90 1.00 -1
> > 15 1.00 282.61-237999.04 282.53 283.81 1.00 -1
> > 16 1.00 289.23-237958.84 288.97 287.68 1.00 -1
> > 17 1.00 278.69-238016.41 279.98 281.25 1.00 -1
> > 18 1.00 278.70-238051.34 277.46 278.73 1.00 -1
> > 19 1.00 298.26-237923.06 299.52 298.19 0.92 -1
> > 20 1.00 293.43-237819.98 296.86 295.53 1.00 -1
> > 21 1.00 285.90-237872.36 285.09 286.38 1.00 -1
> > 22 1.00 271.15-238192.37 270.00 271.23 0.62 -1
> > 23 1.00 272.53-238207.17 272.47 273.71 0.77 -1
> > 24 1.00 290.92-238028.52 291.58 290.28 0.92 -1
> > 25 1.00 286.71-238159.73 286.38 285.09 1.00 -1
> > 26 1.00 284.16-238189.10 283.81 282.53 1.00 -1
> > 27 1.00 272.89-238264.83 271.23 270.00 0.85 -1
> > 28 1.00 278.46-238289.12 278.73 277.46 1.00 -1
> > 29 1.00 272.73-238268.68 273.71 272.47 0.92 -1
> > 30 1.00 281.90-238206.67 281.25 279.98 1.00 -1
> > 31 1.00 279.16-238218.60 276.21 274.96 1.00 -1
> > 32 1.00 273.42-238084.44 274.96 276.21 1.00 -1
> > # exchange 27
> > 1 1.00 305.14-237896.37 306.27 304.91 0.89 -1
> > 2 1.00 306.70-237688.11 304.91 306.27 0.96 -1
> > 3 1.00 299.55-237906.46 299.52 300.86 0.96 -1
> > 4 1.00 308.78-237779.85 307.64 309.01 0.89 -1
> > 5 1.00 303.02-237740.95 302.21 303.56 1.04 -1
> > 6 -1.00 312.04-237760.32 310.44 310.44 0.07 -1
> > 7 1.00 289.44-238148.68 288.97 290.28 1.04 -1
> > 8 1.00 308.40-237883.47 309.01 307.64 0.15 -1
> > 9 1.00 293.62-238039.32 291.58 292.90 0.96 -1
> > 10 1.00 303.22-237972.21 303.56 302.21 0.96 -1
> > 11 1.00 298.26-238017.06 296.86 298.19 1.04 -1
> > 12 1.00 302.52-238053.44 300.86 299.52 0.96 -1
> > 13 1.00 297.91-238061.27 294.21 295.53 1.04 -1
> > 14 1.00 293.39-238165.74 292.90 291.58 0.96 -1
> > 15 1.00 286.69-238367.18 283.81 285.09 1.04 -1
> > 16 1.00 285.33-238372.24 287.68 286.38 0.96 -1
> > 17 1.00 280.09-238415.47 281.25 282.53 1.04 -1
> > 18 1.00 279.14-238456.86 278.73 279.98 1.04 -1
> > 19 1.00 297.69-238179.86 298.19 296.86 0.89 -1
> > 20 1.00 293.78-238363.05 295.53 294.21 0.96 -1
> > 21 1.00 286.04-238315.32 286.38 287.68 1.04 -1
> > 22 1.00 269.92-238495.65 271.23 272.47 0.89 -1
> > 23 1.00 272.51-238431.54 273.71 274.96 0.96 -1
> > 24 1.00 289.51-238323.64 290.28 288.97 0.96 -1
> > 25 1.00 285.80-238400.25 285.09 283.81 0.96 -1
> > 26 1.00 284.11-238504.05 282.53 281.25 0.96 -1
> > 27 -1.00 270.33-238639.41 270.00 270.00 0.59 -1
> > 28 1.00 278.26-238633.26 277.46 276.21 0.96 -1
> > 29 1.00 271.87-238758.14 272.47 271.23 0.74 -1
> > 30 1.00 278.97-238406.37 279.98 278.73 0.96 -1
> > 31 1.00 275.36-238642.13 274.96 273.71 0.96 -1
> > 32 1.00 277.11-238336.79 276.21 277.46 1.04 -1
> > # exchange 28
> > 1 1.00 305.41-238178.28 304.91 303.56 0.93 -1
> > 2 1.00 308.72-237888.75 306.27 307.64 0.93 -1
> > 3 -1.00 299.85-238411.98 300.86 300.86 0.93 -1
> > 4 1.00 308.47-237966.66 309.01 310.44 0.21 -1
> > 5 1.00 302.86-237989.18 303.56 304.91 1.00 -1
> > 6 1.00 310.64-238126.41 310.44 309.01 0.07 -1
> > 7 1.00 291.09-238323.96 290.28 291.58 1.00 -1
> > 8 1.00 306.54-238287.31 307.64 306.27 0.86 -1
> > 9 1.00 292.28-238398.82 292.90 294.21 1.00 -1
> > 10 -1.00 302.07-238374.29 302.21 302.21 1.00 -1
> > 11 1.00 299.33-238367.94 298.19 299.52 0.93 -1
> > 12 1.00 299.74-238329.33 299.52 298.19 0.93 -1
> > 13 1.00 294.48-238329.94 295.53 296.86 1.00 -1
> > 14 1.00 292.88-238512.89 291.58 290.28 0.93 -1
> > 15 1.00 284.54-238592.77 285.09 286.38 1.00 -1
> > 16 1.00 289.06-238586.60 286.38 285.09 1.00 -1
> > 17 1.00 282.18-238604.33 282.53 283.81 1.00 -1
> > 18 1.00 280.42-238498.62 279.98 281.25 1.00 -1
> > 19 1.00 298.42-238339.10 296.86 295.53 1.00 -1
> > 20 1.00 295.23-238501.82 294.21 292.90 1.00 -1
> > 21 1.00 287.96-238622.69 287.68 288.97 1.00 -1
> > 22 1.00 274.59-238791.23 272.47 273.71 0.79 -1
> > 23 1.00 274.34-238732.39 274.96 276.21 1.00 -1
> > 24 1.00 290.89-238503.91 288.97 287.68 1.00 -1
> > 25 1.00 284.40-238719.97 283.81 282.53 1.00 -1
> > 26 1.00 281.12-238697.12 281.25 279.98 1.00 -1
> > 27 1.00 271.44-238981.93 270.00 271.23 0.64 -1
> > 28 1.00 277.56-238877.61 276.21 274.96 1.00 -1
> > 29 1.00 272.58-239072.51 271.23 270.00 0.86 -1
> > 30 1.00 279.19-238902.86 278.73 277.46 1.00 -1
> > 31 1.00 274.58-238952.80 273.71 272.47 0.93 -1
> > 32 1.00 278.29-238672.97 277.46 278.73 1.00 -1
> > # exchange 29
> > 1 1.00 303.10-238482.53 303.56 302.21 0.97 -1
> > 2 1.00 308.47-238268.33 307.64 309.01 0.90 -1
> > 3 1.00 300.90-238576.50 300.86 299.52 0.90 -1
> > 4 -1.00 310.92-238315.71 310.44 310.44 0.07 -1
> > 5 1.00 304.45-238317.36 304.91 306.27 0.97 -1
> > 6 1.00 307.80-238499.68 309.01 307.64 0.21 -1
> > 7 1.00 291.95-238596.78 291.58 292.90 0.97 -1
> > 8 1.00 306.74-238454.39 306.27 304.91 0.90 -1
> > 9 1.00 294.77-238569.62 294.21 295.53 1.03 -1
> > 10 1.00 303.24-238531.15 302.21 303.56 1.03 -1
> > 11 1.00 299.01-238638.43 299.52 300.86 0.97 -1
> > 12 1.00 299.36-238835.63 298.19 296.86 0.90 -1
> > 13 1.00 298.09-238588.55 296.86 298.19 1.03 -1
> > 14 1.00 291.63-238777.70 290.28 288.97 0.97 -1
> > 15 1.00 286.85-239032.37 286.38 287.68 1.03 -1
> > 16 1.00 285.69-238846.49 285.09 283.81 0.97 -1
> > 17 1.00 282.94-238892.18 283.81 285.09 1.03 -1
> > 18 1.00 281.44-238894.57 281.25 282.53 1.03 -1
> > 19 1.00 296.81-238719.29 295.53 294.21 0.97 -1
> > 20 1.00 293.05-238860.89 292.90 291.58 0.97 -1
> > 21 1.00 286.63-238769.89 288.97 290.28 1.03 -1
> > 22 1.00 276.10-238983.43 273.71 274.96 0.97 -1
> > 23 1.00 278.03-238930.08 276.21 277.46 1.03 -1
> > 24 1.00 286.91-238958.25 287.68 286.38 0.97 -1
> > 25 1.00 282.26-239046.26 282.53 281.25 0.97 -1
> > 26 1.00 279.78-239123.91 279.98 278.73 0.97 -1
> > 27 1.00 273.78-239151.24 271.23 272.47 0.90 -1
> > 28 1.00 275.98-239171.49 274.96 273.71 0.97 -1
> > 29 -1.00 269.99-239317.35 270.00 270.00 0.62 -1
> > 30 1.00 276.91-239191.40 277.46 276.21 0.97 -1
> > 31 1.00 272.73-239255.54 272.47 271.23 0.76 -1
> > 32 1.00 279.96-238888.03 278.73 279.98 1.03 -1
> > # exchange 30
> > 1 1.00 302.64-238842.01 302.21 300.86 1.00 -1
> > 2 1.00 308.63-238427.17 309.01 310.44 0.27 -1
> > 3 1.00 299.84-238911.95 299.52 298.19 0.93 -1
> > 4 1.00 309.86-238515.73 310.44 309.01 0.07 -1
> > 5 1.00 307.42-238560.64 306.27 307.64 0.93 -1
> > 6 1.00 307.48-238702.43 307.64 306.27 0.87 -1
> > 7 1.00 292.53-238839.87 292.90 294.21 1.00 -1
> > 8 1.00 306.00-238777.41 304.91 303.56 0.93 -1
> > 9 1.00 297.32-238947.72 295.53 296.86 1.00 -1
> > 10 1.00 304.05-238883.82 303.56 304.91 1.00 -1
> > 11 1.00 302.57-238780.54 300.86 302.21 0.93 -1
> > 12 1.00 292.21-238910.66 296.86 295.53 1.00 -1
> > 13 1.00 298.97-238780.23 298.19 299.52 0.93 -1
> > 14 1.00 286.86-239171.01 288.97 287.68 1.00 -1
> > 15 1.00 290.28-239150.80 287.68 288.97 1.00 -1
> > 16 1.00 282.76-239323.47 283.81 282.53 1.00 -1
> > 17 1.00 284.27-239063.46 285.09 286.38 1.00 -1
> > 18 1.00 281.82-239049.67 282.53 283.81 1.00 -1
> > 19 1.00 292.78-239024.98 294.21 292.90 1.00 -1
> > 20 1.00 293.24-239149.18 291.58 290.28 0.93 -1
> > 21 1.00 291.56-239013.66 290.28 291.58 1.00 -1
> > 22 1.00 276.39-239397.26 274.96 276.21 1.00 -1
> > 23 1.00 278.04-239172.39 277.46 278.73 1.00 -1
> > 24 1.00 287.81-239189.88 286.38 285.09 1.00 -1
> > 25 1.00 281.80-239499.51 281.25 279.98 1.00 -1
> > 26 1.00 279.53-239167.74 278.73 277.46 1.00 -1
> > 27 1.00 272.13-239418.19 272.47 273.71 0.80 -1
> > 28 1.00 273.73-239459.18 273.71 272.47 0.93 -1
> > 29 1.00 269.25-239534.80 270.00 271.23 0.67 -1
> > 30 1.00 278.19-239456.51 276.21 274.96 1.00 -1
> > 31 1.00 267.89-239471.35 271.23 270.00 0.87 -1
> > 32 1.00 282.43-239161.13 279.98 281.25 1.00 -1
> > # exchange 31
> > 1 1.00 301.00-238974.09 300.86 299.52 0.90 -1
> > 2 -1.00 309.61-238660.96 310.44 310.44 0.06 -1
> > 3 1.00 299.18-239060.07 298.19 296.86 0.90 -1
> > 4 1.00 310.05-238867.09 309.01 307.64 0.26 -1
> > 5 1.00 305.97-238751.83 307.64 309.01 0.90 -1
> > 6 1.00 303.80-238862.17 306.27 304.91 0.90 -1
> > 7 1.00 294.92-239133.23 294.21 295.53 1.03 -1
> > 8 1.00 300.79-239134.89 303.56 302.21 0.97 -1
> > 9 1.00 295.27-239078.59 296.86 298.19 1.03 -1
> > 10 1.00 307.38-238976.05 304.91 306.27 0.97 -1
> > 11 1.00 299.93-239007.75 302.21 303.56 1.03 -1
> > 12 1.00 296.23-239266.13 295.53 294.21 0.97 -1
> > 13 1.00 300.31-238964.11 299.52 300.86 0.97 -1
> > 14 1.00 288.87-239491.68 287.68 286.38 0.97 -1
> > 15 1.00 288.87-239181.78 288.97 290.28 1.03 -1
> > 16 1.00 283.85-239447.44 282.53 281.25 0.97 -1
> > 17 1.00 286.93-239387.00 286.38 287.68 1.03 -1
> > 18 1.00 285.28-239293.13 283.81 285.09 1.03 -1
> > 19 1.00 294.38-239262.60 292.90 291.58 0.97 -1
> > 20 1.00 291.41-239473.95 290.28 288.97 0.97 -1
> > 21 1.00 291.99-239025.10 291.58 292.90 0.97 -1
> > 22 1.00 277.99-239464.65 276.21 277.46 1.03 -1
> > 23 1.00 280.21-239389.24 278.73 279.98 1.03 -1
> > 24 1.00 285.12-239418.39 285.09 283.81 0.97 -1
> > 25 1.00 279.17-239630.47 279.98 278.73 0.97 -1
> > 26 1.00 276.92-239490.22 277.46 276.21 0.97 -1
> > 27 -1.00 273.11-239656.31 273.71 273.71 0.90 -1
> > 28 1.00 272.29-239793.97 272.47 271.23 0.77 -1
> > 29 1.00 271.67-239750.30 271.23 272.47 0.90 -1
> > 30 -1.00 273.12-239533.78 274.96 274.96 0.97 -1
> > 31 -1.00 268.90-239618.69 270.00 270.00 0.65 -1
> > 32 1.00 281.96-239330.79 281.25 282.53 1.03 -1
> > # exchange 32
> > 1 1.00 299.58-239343.43 299.52 298.19 0.94 -1
> > 2 1.00 311.50-238980.95 310.44 309.01 0.06 -1
> > 3 1.00 295.85-239184.29 296.86 295.53 1.00 -1
> > 4 -1.00 308.17-239136.45 307.64 307.64 0.88 -1
> > 5 1.00 308.06-238988.58 309.01 310.44 0.31 -1
> > 6 1.00 305.13-239138.99 304.91 303.56 0.94 -1
> > 7 1.00 297.85-239308.56 295.53 296.86 1.00 -1
> > 8 1.00 301.01-239380.21 302.21 300.86 1.00 -1
> > 9 1.00 298.53-239203.29 298.19 299.52 0.94 -1
> > 10 -1.00 304.70-239232.45 306.27 306.27 0.88 -1
> > 11 1.00 302.69-239202.78 303.56 304.91 1.00 -1
> > 12 1.00 294.94-239499.66 294.21 292.90 1.00 -1
> > 13 1.00 300.69-239395.23 300.86 302.21 0.94 -1
> > 14 1.00 286.37-239695.11 286.38 285.09 1.00 -1
> > 15 1.00 291.36-239520.08 290.28 291.58 1.00 -1
> > 16 1.00 281.85-239685.86 281.25 279.98 1.00 -1
> > 17 1.00 286.91-239521.64 287.68 288.97 1.00 -1
> > 18 1.00 285.86-239469.74 285.09 286.38 1.00 -1
> > 19 1.00 291.53-239557.96 291.58 290.28 0.94 -1
> > 20 1.00 287.61-239612.47 288.97 287.68 1.00 -1
> > 21 1.00 295.50-239511.96 292.90 294.21 1.00 -1
> > 22 1.00 277.08-239728.20 277.46 278.73 1.00 -1
> > 23 1.00 281.02-239549.47 279.98 281.25 1.00 -1
> > 24 1.00 285.24-239811.81 283.81 282.53 1.00 -1
> > 25 1.00 280.54-239919.66 278.73 277.46 1.00 -1
> > 26 1.00 275.03-239906.59 276.21 274.96 1.00 -1
> > 27 -1.00 273.96-239787.93 273.71 273.71 0.88 -1
> > 28 1.00 271.41-239907.75 271.23 270.00 0.88 -1
> > 29 -1.00 272.49-239881.87 272.47 272.47 0.75 -1
> > 30 1.00 273.86-239793.13 274.96 276.21 1.00 -1
> > 31 1.00 270.74-239929.02 270.00 271.23 0.69 -1
> > 32 1.00 284.17-239559.23 282.53 283.81 1.00 -1
> > # exchange 33
> > 1 1.00 298.56-239647.71 298.19 296.86 0.91 -1
> > 2 1.00 310.32-239222.61 309.01 307.64 0.30 -1
> > 3 1.00 294.15-239565.38 295.53 294.21 0.97 -1
> > 4 1.00 303.38-239211.71 307.64 309.01 0.91 -1
> > 5 -1.00 311.39-239214.75 310.44 310.44 0.06 -1
> > 6 1.00 303.15-239587.23 303.56 302.21 0.97 -1
> > 7 1.00 295.82-239452.66 296.86 298.19 1.03 -1
> > 8 1.00 301.75-239706.01 300.86 299.52 0.91 -1
> > 9 1.00 299.23-239590.40 299.52 300.86 0.97 -1
> > 10 1.00 306.48-239596.64 306.27 304.91 0.85 -1
> > 11 1.00 304.11-239317.37 304.91 306.27 0.97 -1
> > 12 1.00 295.12-239733.48 292.90 291.58 0.97 -1
> > 13 1.00 302.37-239381.64 302.21 303.56 1.03 -1
> > 14 1.00 285.43-239993.86 285.09 283.81 0.97 -1
> > 15 1.00 293.03-239827.37 291.58 292.90 0.97 -1
> > 16 1.00 281.71-240076.80 279.98 278.73 0.97 -1
> > 17 1.00 287.46-239707.00 288.97 290.28 1.03 -1
> > 18 1.00 287.92-239662.53 286.38 287.68 1.03 -1
> > 19 1.00 289.38-239765.38 290.28 288.97 0.97 -1
> > 20 1.00 287.47-239790.23 287.68 286.38 0.97 -1
> > 21 1.00 293.81-239572.60 294.21 295.53 1.03 -1
> > 22 1.00 279.07-239939.90 278.73 279.98 1.03 -1
> > 23 1.00 279.45-239795.77 281.25 282.53 1.03 -1
> > 24 1.00 282.05-240026.98 282.53 281.25 0.97 -1
> > 25 1.00 280.62-240229.59 277.46 276.21 0.97 -1
> > 26 1.00 276.37-240004.49 274.96 273.71 0.97 -1
> > 27 1.00 274.39-240117.97 273.71 274.96 0.91 -1
> > 28 -1.00 271.27-240176.99 270.00 270.00 0.67 -1
> > 29 1.00 272.88-240227.77 272.47 271.23 0.73 -1
> > 30 1.00 277.02-240107.91 276.21 277.46 1.03 -1
> > 31 1.00 271.63-240007.57 271.23 272.47 0.91 -1
> > 32 1.00 283.63-239721.84 283.81 285.09 1.03 -1
> >
> > Temperatures were selected using: http://folding.bmc.uu.se/remd/
> > The temperatures are:
> > 270.00, 271.24, 272.48, 273.73, 274.98, 276.24, 277.50, 278.76, 280.04,
> > 281.31, 282.59, 283.87, 285.17, 286.46, 287.76, 289.06, 290.37, 291.68,
> > 293.00, 294.32, 295.65, 296.98, 298.32, 299.66, 301.01, 302.35, 303.71,
> > 305.07, 306.43, 307.81, 309.18, 310.57
> >
> > These temperatures are based on 102229 degrees of freedom for the system
> > and a desired exchange probability of .22. According to my mdout files,
> > the system actually has 101423 degrees of freedom. So I think the
> > temperatures may be a bit off, but I would be very surprised if they were
> > responsible for anything as drastically weird as what I'm seeing.
> >
> > Has anybody seen these types of results before? What was the the cause?
> > How did yo solve it?
> >
> > Christopher Thiebaut
> > Graduate Student
> > Purdue University
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------------------------------------------------------
Christina Bergonzo, PhD
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
30 South 2000 East, Rm. 201
Salt Lake City, UT 84112-5820
Office: L.S. Skaggs Pharmacy Research Institute, Rm.4290
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652 / Fax: (801) 585-6208
---------------------------------------------------------------------------------------
------------------------------
Message: 5
Date: Mon, 7 Apr 2014 16:21:54 -0400 (EDT)
From: Christopher A Thiebaut <cthieba.purdue.edu>
Subject: Re: [AMBER] Really Weird Problem with Replica Exchange
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<1723432075.88845.1396902114254.JavaMail.root.mailhub055.itcs.purdue.edu>
Content-Type: text/plain; charset=utf-8
Christina,
The reason for the unuasually low high temperature is that I am actually trying to increase sampling of the water positions rather than the protein itself. Previously, we have compared the water positions around the active site derrived from MD simulations with those from the crystal structures and were not able to reproduce the experimental water positions. We think this may be because the crystal structures are taken at very low temperatures (But obviously a simple MD simulation of frozen water won't give us any change in water position). There are about 5,000 protein atoms and about 15,000 water molecules. I have SHAKEn the bonds to hydrogen within the protein to allow for a longer timestep dt=0.002.
Christopher
----- Original Message -----
From: "Christina Bergonzo" <cbergonzo.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Monday, April 7, 2014 4:08:28 PM
Subject: Re: [AMBER] Really Weird Problem with Replica Exchange
Hi Christopher,
Even if you have independently equilibrated the starting structures, it can
take a while for the exchange probability to average out. This is system
size dependent, and could take much longer than 30-ish exchanges. The
exchange probability should start out at 0, though, and rise to whatever
acceptance % you set up. The high initial acceptance tells me these
replicas may be set up too closely, though I have used the same temperature
generator before and gotten a good distribution out of it.
In addition to what Carlos asked, how many atoms/how many water molecules
are in your system? And what are you trying to sample here? A high
temperature of ~300K seems too low to enhance sampling all that much. The
T-REMD tutorial suggests using a range potentially up to 600K:
http://ambermd.org/tutorials/advanced/tutorial7/
-Christina
On Mon, Apr 7, 2014 at 2:02 PM, Christopher A Thiebaut
<cthieba.purdue.edu>wrote:
> The initial structure was thermolysin with no ligand bound (will be doing
> simulations with a variety of ligands bound later on) solvated in a TIP3P
> truncated octahedron with periodic boundary conditions. I minimized the
> solvent with the protein restrained, then minimized the system as a whole,
> did a brief NVT simulation to get my system up to a reasonabe temperature,
> which was in the middle of my range. Then I did a short NPT simulation (at
> the same temperature, 1 atm pressure) to correct the density. Technically,
> I know that density won't be quite right at most of my temperatures but I
> don't have a huge temperature range so I don't think it should really be
> troublingly off either. Then I did 32 separate equilibrations based on that
> structure (at the replica exchange temperatures) before finally moving to
> the replica exchange simulation.
>
> Christopher Thiebaut
> Graduate Student
> Purdue University
> ----- Original Message -----
> From: "Carlos Simmerling" <carlos.simmerling.gmail.com>
> To: "AMBER Mailing List" <amber.ambermd.org>
> Sent: Monday, April 7, 2014 3:48:18 PM
> Subject: Re: [AMBER] Really Weird Problem with Replica Exchange
>
> what were the initial structures? were they pre-equilibrated that the right
> Ts? tell us more about how you got to this point...
>
>
> On Mon, Apr 7, 2014 at 2:58 PM, Christopher A Thiebaut
> <cthieba.purdue.edu>wrote:
>
> > Helllo all,
> >
> > I am having what I imagine to be a very unusual problem running replica
> > exchange of thermolysin solvated with explicit TIP3P water.
> > The simulations will run without any error messages, but I am sure the
> > results I am seeing are not meaningful because most replicas are
> exchanging
> > at most exchange attempts and even more so because the volocity scaling
> is
> > always 1.0 (meaning the volocites are not changed at all), except once
> > during the first exchange. In addition, the total potential energy seems
> > to be slowly increasing throughout the simulation which also should not
> be
> > happening.
> >
> > Here's a sample of my rem.log file so you can see what I'm talking about:
> > # Rep#, Velocity Scaling, T, Eptot, Temp0, NewTemp0, Success rate
> (i,i+1),
> > ResStruct#
> > # exchange 1
> > 1 1.07 0.00-158275.28 270.00 310.44 0.00 -1
> > 2 1.00 0.00-158841.35 271.23 272.47 2.00 -1
> > 3 1.00 0.00-159708.30 272.47 271.23 0.00 -1
> > 4 1.00 0.00-159547.14 273.71 274.96 2.00 -1
> > 5 1.00 0.00-159457.82 274.96 273.71 0.00 -1
> > 6 1.00 0.00-160730.25 276.21 277.46 2.00 -1
> > 7 1.00 0.00-160858.37 277.46 276.21 0.00 -1
> > 8 1.00 0.00-161155.52 278.73 279.98 2.00 -1
> > 9 1.00 0.00-161044.87 279.98 278.73 0.00 -1
> > 10 1.00 0.00-161039.89 281.25 282.53 2.00 -1
> > 11 1.00 0.00-161096.24 282.53 281.25 0.00 -1
> > 12 1.00 0.00-162494.74 283.81 285.09 2.00 -1
> > 13 1.00 0.00-162767.85 285.09 283.81 0.00 -1
> > 14 1.00 0.00-161902.49 286.38 287.68 2.00 -1
> > 15 1.00 0.00-163145.99 287.68 286.38 0.00 -1
> > 16 1.00 0.00-162901.03 288.97 290.28 2.00 -1
> > 17 1.00 0.00-164106.69 290.28 288.97 0.00 -1
> > 18 -1.00 0.00-163819.64 291.58 291.58 0.00 -1
> > 19 -1.00 0.00-163549.67 292.90 292.90 0.00 -1
> > 20 1.00 0.00-163950.79 294.21 295.53 2.00 -1
> > 21 1.00 0.00-164690.76 295.53 294.21 0.00 -1
> > 22 1.00 0.00-165187.80 296.86 298.19 2.00 -1
> > 23 1.00 0.00-165377.17 298.19 296.86 0.00 -1
> > 24 -1.00 0.00-164848.36 299.52 299.52 0.00 -1
> > 25 -1.00 0.00-164797.83 300.86 300.86 0.00 -1
> > 26 1.00 0.00-165237.92 302.21 303.56 2.00 -1
> > 27 1.00 0.00-166216.65 303.56 302.21 0.00 -1
> > 28 1.00 0.00-166127.19 304.91 306.27 2.00 -1
> > 29 1.00 0.00-167327.09 306.27 304.91 0.00 -1
> > 30 1.00 0.00-166545.00 307.64 309.01 2.00 -1
> > 31 1.00 0.00-168071.75 309.01 307.64 0.00 -1
> > 32 0.93 0.00-167178.34 310.44 270.00 2.00 -1
> > ......................................................................
> > # exchange 25
> > 1 1.00 309.91-237311.34 309.01 307.64 0.08 -1
> > 2 1.00 304.26-237005.16 302.21 303.56 1.04 -1
> > 3 1.00 296.00-237356.49 296.86 298.19 1.04 -1
> > 4 1.00 304.33-237213.57 304.91 306.27 0.96 -1
> > 5 1.00 300.61-237074.41 299.52 300.86 0.96 -1
> > 6 1.00 306.71-237010.94 307.64 309.01 0.88 -1
> > 7 1.00 288.23-237533.96 286.38 287.68 1.04 -1
> > 8 -1.00 309.85-237252.49 310.44 310.44 0.08 -1
> > 9 1.00 289.99-237569.69 288.97 290.28 1.04 -1
> > 10 1.00 307.03-237289.10 306.27 304.91 0.88 -1
> > 11 1.00 296.78-237439.24 294.21 295.53 1.04 -1
> > 12 1.00 302.80-237548.07 303.56 302.21 0.96 -1
> > 13 1.00 291.19-237476.28 291.58 292.90 0.96 -1
> > 14 1.00 298.13-237536.76 295.53 294.21 0.96 -1
> > 15 1.00 284.22-237758.43 281.25 282.53 1.04 -1
> > 16 1.00 291.28-237590.61 290.28 288.97 0.96 -1
> > 17 1.00 277.07-237711.31 278.73 279.98 1.04 -1
> > 18 1.00 277.52-237747.34 276.21 277.46 1.04 -1
> > 19 1.00 300.95-237501.70 300.86 299.52 0.96 -1
> > 20 1.00 297.03-237561.12 298.19 296.86 0.88 -1
> > 21 1.00 282.63-237651.93 283.81 285.09 1.04 -1
> > 22 -1.00 270.53-238135.36 270.00 270.00 0.56 -1
> > 23 1.00 272.50-237928.60 271.23 272.47 0.88 -1
> > 24 1.00 292.11-237641.94 292.90 291.58 0.96 -1
> > 25 1.00 288.51-237686.39 287.68 286.38 0.96 -1
> > 26 1.00 285.15-237838.02 285.09 283.81 0.96 -1
> > 27 1.00 269.94-237998.93 272.47 271.23 0.72 -1
> > 28 1.00 278.70-237910.14 279.98 278.73 0.96 -1
> > 29 1.00 275.61-238021.61 274.96 273.71 0.96 -1
> > 30 1.00 282.57-237916.92 282.53 281.25 0.96 -1
> > 31 1.00 276.88-238031.26 277.46 276.21 0.96 -1
> > 32 1.00 273.65-237788.60 273.71 274.96 0.96 -1
> > # exchange 26
> > 1 1.00 309.43-237528.66 307.64 306.27 0.85 -1
> > 2 1.00 303.95-237551.08 303.56 304.91 1.00 -1
> > 3 1.00 297.95-237809.91 298.19 299.52 0.92 -1
> > 4 1.00 306.31-237657.13 306.27 307.64 0.92 -1
> > 5 1.00 299.96-237577.66 300.86 302.21 1.00 -1
> > 6 1.00 308.95-237472.73 309.01 310.44 0.15 -1
> > 7 1.00 286.56-237844.08 287.68 288.97 1.00 -1
> > 8 1.00 310.00-237519.31 310.44 309.01 0.08 -1
> > 9 1.00 291.81-237729.64 290.28 291.58 1.00 -1
> > 10 1.00 303.70-237715.75 304.91 303.56 0.92 -1
> > 11 1.00 296.62-237700.83 295.53 296.86 1.00 -1
> > 12 1.00 303.16-237772.77 302.21 300.86 1.00 -1
> > 13 1.00 292.60-237770.36 292.90 294.21 1.00 -1
> > 14 1.00 293.41-237816.24 294.21 292.90 1.00 -1
> > 15 1.00 282.61-237999.04 282.53 283.81 1.00 -1
> > 16 1.00 289.23-237958.84 288.97 287.68 1.00 -1
> > 17 1.00 278.69-238016.41 279.98 281.25 1.00 -1
> > 18 1.00 278.70-238051.34 277.46 278.73 1.00 -1
> > 19 1.00 298.26-237923.06 299.52 298.19 0.92 -1
> > 20 1.00 293.43-237819.98 296.86 295.53 1.00 -1
> > 21 1.00 285.90-237872.36 285.09 286.38 1.00 -1
> > 22 1.00 271.15-238192.37 270.00 271.23 0.62 -1
> > 23 1.00 272.53-238207.17 272.47 273.71 0.77 -1
> > 24 1.00 290.92-238028.52 291.58 290.28 0.92 -1
> > 25 1.00 286.71-238159.73 286.38 285.09 1.00 -1
> > 26 1.00 284.16-238189.10 283.81 282.53 1.00 -1
> > 27 1.00 272.89-238264.83 271.23 270.00 0.85 -1
> > 28 1.00 278.46-238289.12 278.73 277.46 1.00 -1
> > 29 1.00 272.73-238268.68 273.71 272.47 0.92 -1
> > 30 1.00 281.90-238206.67 281.25 279.98 1.00 -1
> > 31 1.00 279.16-238218.60 276.21 274.96 1.00 -1
> > 32 1.00 273.42-238084.44 274.96 276.21 1.00 -1
> > # exchange 27
> > 1 1.00 305.14-237896.37 306.27 304.91 0.89 -1
> > 2 1.00 306.70-237688.11 304.91 306.27 0.96 -1
> > 3 1.00 299.55-237906.46 299.52 300.86 0.96 -1
> > 4 1.00 308.78-237779.85 307.64 309.01 0.89 -1
> > 5 1.00 303.02-237740.95 302.21 303.56 1.04 -1
> > 6 -1.00 312.04-237760.32 310.44 310.44 0.07 -1
> > 7 1.00 289.44-238148.68 288.97 290.28 1.04 -1
> > 8 1.00 308.40-237883.47 309.01 307.64 0.15 -1
> > 9 1.00 293.62-238039.32 291.58 292.90 0.96 -1
> > 10 1.00 303.22-237972.21 303.56 302.21 0.96 -1
> > 11 1.00 298.26-238017.06 296.86 298.19 1.04 -1
> > 12 1.00 302.52-238053.44 300.86 299.52 0.96 -1
> > 13 1.00 297.91-238061.27 294.21 295.53 1.04 -1
> > 14 1.00 293.39-238165.74 292.90 291.58 0.96 -1
> > 15 1.00 286.69-238367.18 283.81 285.09 1.04 -1
> > 16 1.00 285.33-238372.24 287.68 286.38 0.96 -1
> > 17 1.00 280.09-238415.47 281.25 282.53 1.04 -1
> > 18 1.00 279.14-238456.86 278.73 279.98 1.04 -1
> > 19 1.00 297.69-238179.86 298.19 296.86 0.89 -1
> > 20 1.00 293.78-238363.05 295.53 294.21 0.96 -1
> > 21 1.00 286.04-238315.32 286.38 287.68 1.04 -1
> > 22 1.00 269.92-238495.65 271.23 272.47 0.89 -1
> > 23 1.00 272.51-238431.54 273.71 274.96 0.96 -1
> > 24 1.00 289.51-238323.64 290.28 288.97 0.96 -1
> > 25 1.00 285.80-238400.25 285.09 283.81 0.96 -1
> > 26 1.00 284.11-238504.05 282.53 281.25 0.96 -1
> > 27 -1.00 270.33-238639.41 270.00 270.00 0.59 -1
> > 28 1.00 278.26-238633.26 277.46 276.21 0.96 -1
> > 29 1.00 271.87-238758.14 272.47 271.23 0.74 -1
> > 30 1.00 278.97-238406.37 279.98 278.73 0.96 -1
> > 31 1.00 275.36-238642.13 274.96 273.71 0.96 -1
> > 32 1.00 277.11-238336.79 276.21 277.46 1.04 -1
> > # exchange 28
> > 1 1.00 305.41-238178.28 304.91 303.56 0.93 -1
> > 2 1.00 308.72-237888.75 306.27 307.64 0.93 -1
> > 3 -1.00 299.85-238411.98 300.86 300.86 0.93 -1
> > 4 1.00 308.47-237966.66 309.01 310.44 0.21 -1
> > 5 1.00 302.86-237989.18 303.56 304.91 1.00 -1
> > 6 1.00 310.64-238126.41 310.44 309.01 0.07 -1
> > 7 1.00 291.09-238323.96 290.28 291.58 1.00 -1
> > 8 1.00 306.54-238287.31 307.64 306.27 0.86 -1
> > 9 1.00 292.28-238398.82 292.90 294.21 1.00 -1
> > 10 -1.00 302.07-238374.29 302.21 302.21 1.00 -1
> > 11 1.00 299.33-238367.94 298.19 299.52 0.93 -1
> > 12 1.00 299.74-238329.33 299.52 298.19 0.93 -1
> > 13 1.00 294.48-238329.94 295.53 296.86 1.00 -1
> > 14 1.00 292.88-238512.89 291.58 290.28 0.93 -1
> > 15 1.00 284.54-238592.77 285.09 286.38 1.00 -1
> > 16 1.00 289.06-238586.60 286.38 285.09 1.00 -1
> > 17 1.00 282.18-238604.33 282.53 283.81 1.00 -1
> > 18 1.00 280.42-238498.62 279.98 281.25 1.00 -1
> > 19 1.00 298.42-238339.10 296.86 295.53 1.00 -1
> > 20 1.00 295.23-238501.82 294.21 292.90 1.00 -1
> > 21 1.00 287.96-238622.69 287.68 288.97 1.00 -1
> > 22 1.00 274.59-238791.23 272.47 273.71 0.79 -1
> > 23 1.00 274.34-238732.39 274.96 276.21 1.00 -1
> > 24 1.00 290.89-238503.91 288.97 287.68 1.00 -1
> > 25 1.00 284.40-238719.97 283.81 282.53 1.00 -1
> > 26 1.00 281.12-238697.12 281.25 279.98 1.00 -1
> > 27 1.00 271.44-238981.93 270.00 271.23 0.64 -1
> > 28 1.00 277.56-238877.61 276.21 274.96 1.00 -1
> > 29 1.00 272.58-239072.51 271.23 270.00 0.86 -1
> > 30 1.00 279.19-238902.86 278.73 277.46 1.00 -1
> > 31 1.00 274.58-238952.80 273.71 272.47 0.93 -1
> > 32 1.00 278.29-238672.97 277.46 278.73 1.00 -1
> > # exchange 29
> > 1 1.00 303.10-238482.53 303.56 302.21 0.97 -1
> > 2 1.00 308.47-238268.33 307.64 309.01 0.90 -1
> > 3 1.00 300.90-238576.50 300.86 299.52 0.90 -1
> > 4 -1.00 310.92-238315.71 310.44 310.44 0.07 -1
> > 5 1.00 304.45-238317.36 304.91 306.27 0.97 -1
> > 6 1.00 307.80-238499.68 309.01 307.64 0.21 -1
> > 7 1.00 291.95-238596.78 291.58 292.90 0.97 -1
> > 8 1.00 306.74-238454.39 306.27 304.91 0.90 -1
> > 9 1.00 294.77-238569.62 294.21 295.53 1.03 -1
> > 10 1.00 303.24-238531.15 302.21 303.56 1.03 -1
> > 11 1.00 299.01-238638.43 299.52 300.86 0.97 -1
> > 12 1.00 299.36-238835.63 298.19 296.86 0.90 -1
> > 13 1.00 298.09-238588.55 296.86 298.19 1.03 -1
> > 14 1.00 291.63-238777.70 290.28 288.97 0.97 -1
> > 15 1.00 286.85-239032.37 286.38 287.68 1.03 -1
> > 16 1.00 285.69-238846.49 285.09 283.81 0.97 -1
> > 17 1.00 282.94-238892.18 283.81 285.09 1.03 -1
> > 18 1.00 281.44-238894.57 281.25 282.53 1.03 -1
> > 19 1.00 296.81-238719.29 295.53 294.21 0.97 -1
> > 20 1.00 293.05-238860.89 292.90 291.58 0.97 -1
> > 21 1.00 286.63-238769.89 288.97 290.28 1.03 -1
> > 22 1.00 276.10-238983.43 273.71 274.96 0.97 -1
> > 23 1.00 278.03-238930.08 276.21 277.46 1.03 -1
> > 24 1.00 286.91-238958.25 287.68 286.38 0.97 -1
> > 25 1.00 282.26-239046.26 282.53 281.25 0.97 -1
> > 26 1.00 279.78-239123.91 279.98 278.73 0.97 -1
> > 27 1.00 273.78-239151.24 271.23 272.47 0.90 -1
> > 28 1.00 275.98-239171.49 274.96 273.71 0.97 -1
> > 29 -1.00 269.99-239317.35 270.00 270.00 0.62 -1
> > 30 1.00 276.91-239191.40 277.46 276.21 0.97 -1
> > 31 1.00 272.73-239255.54 272.47 271.23 0.76 -1
> > 32 1.00 279.96-238888.03 278.73 279.98 1.03 -1
> > # exchange 30
> > 1 1.00 302.64-238842.01 302.21 300.86 1.00 -1
> > 2 1.00 308.63-238427.17 309.01 310.44 0.27 -1
> > 3 1.00 299.84-238911.95 299.52 298.19 0.93 -1
> > 4 1.00 309.86-238515.73 310.44 309.01 0.07 -1
> > 5 1.00 307.42-238560.64 306.27 307.64 0.93 -1
> > 6 1.00 307.48-238702.43 307.64 306.27 0.87 -1
> > 7 1.00 292.53-238839.87 292.90 294.21 1.00 -1
> > 8 1.00 306.00-238777.41 304.91 303.56 0.93 -1
> > 9 1.00 297.32-238947.72 295.53 296.86 1.00 -1
> > 10 1.00 304.05-238883.82 303.56 304.91 1.00 -1
> > 11 1.00 302.57-238780.54 300.86 302.21 0.93 -1
> > 12 1.00 292.21-238910.66 296.86 295.53 1.00 -1
> > 13 1.00 298.97-238780.23 298.19 299.52 0.93 -1
> > 14 1.00 286.86-239171.01 288.97 287.68 1.00 -1
> > 15 1.00 290.28-239150.80 287.68 288.97 1.00 -1
> > 16 1.00 282.76-239323.47 283.81 282.53 1.00 -1
> > 17 1.00 284.27-239063.46 285.09 286.38 1.00 -1
> > 18 1.00 281.82-239049.67 282.53 283.81 1.00 -1
> > 19 1.00 292.78-239024.98 294.21 292.90 1.00 -1
> > 20 1.00 293.24-239149.18 291.58 290.28 0.93 -1
> > 21 1.00 291.56-239013.66 290.28 291.58 1.00 -1
> > 22 1.00 276.39-239397.26 274.96 276.21 1.00 -1
> > 23 1.00 278.04-239172.39 277.46 278.73 1.00 -1
> > 24 1.00 287.81-239189.88 286.38 285.09 1.00 -1
> > 25 1.00 281.80-239499.51 281.25 279.98 1.00 -1
> > 26 1.00 279.53-239167.74 278.73 277.46 1.00 -1
> > 27 1.00 272.13-239418.19 272.47 273.71 0.80 -1
> > 28 1.00 273.73-239459.18 273.71 272.47 0.93 -1
> > 29 1.00 269.25-239534.80 270.00 271.23 0.67 -1
> > 30 1.00 278.19-239456.51 276.21 274.96 1.00 -1
> > 31 1.00 267.89-239471.35 271.23 270.00 0.87 -1
> > 32 1.00 282.43-239161.13 279.98 281.25 1.00 -1
> > # exchange 31
> > 1 1.00 301.00-238974.09 300.86 299.52 0.90 -1
> > 2 -1.00 309.61-238660.96 310.44 310.44 0.06 -1
> > 3 1.00 299.18-239060.07 298.19 296.86 0.90 -1
> > 4 1.00 310.05-238867.09 309.01 307.64 0.26 -1
> > 5 1.00 305.97-238751.83 307.64 309.01 0.90 -1
> > 6 1.00 303.80-238862.17 306.27 304.91 0.90 -1
> > 7 1.00 294.92-239133.23 294.21 295.53 1.03 -1
> > 8 1.00 300.79-239134.89 303.56 302.21 0.97 -1
> > 9 1.00 295.27-239078.59 296.86 298.19 1.03 -1
> > 10 1.00 307.38-238976.05 304.91 306.27 0.97 -1
> > 11 1.00 299.93-239007.75 302.21 303.56 1.03 -1
> > 12 1.00 296.23-239266.13 295.53 294.21 0.97 -1
> > 13 1.00 300.31-238964.11 299.52 300.86 0.97 -1
> > 14 1.00 288.87-239491.68 287.68 286.38 0.97 -1
> > 15 1.00 288.87-239181.78 288.97 290.28 1.03 -1
> > 16 1.00 283.85-239447.44 282.53 281.25 0.97 -1
> > 17 1.00 286.93-239387.00 286.38 287.68 1.03 -1
> > 18 1.00 285.28-239293.13 283.81 285.09 1.03 -1
> > 19 1.00 294.38-239262.60 292.90 291.58 0.97 -1
> > 20 1.00 291.41-239473.95 290.28 288.97 0.97 -1
> > 21 1.00 291.99-239025.10 291.58 292.90 0.97 -1
> > 22 1.00 277.99-239464.65 276.21 277.46 1.03 -1
> > 23 1.00 280.21-239389.24 278.73 279.98 1.03 -1
> > 24 1.00 285.12-239418.39 285.09 283.81 0.97 -1
> > 25 1.00 279.17-239630.47 279.98 278.73 0.97 -1
> > 26 1.00 276.92-239490.22 277.46 276.21 0.97 -1
> > 27 -1.00 273.11-239656.31 273.71 273.71 0.90 -1
> > 28 1.00 272.29-239793.97 272.47 271.23 0.77 -1
> > 29 1.00 271.67-239750.30 271.23 272.47 0.90 -1
> > 30 -1.00 273.12-239533.78 274.96 274.96 0.97 -1
> > 31 -1.00 268.90-239618.69 270.00 270.00 0.65 -1
> > 32 1.00 281.96-239330.79 281.25 282.53 1.03 -1
> > # exchange 32
> > 1 1.00 299.58-239343.43 299.52 298.19 0.94 -1
> > 2 1.00 311.50-238980.95 310.44 309.01 0.06 -1
> > 3 1.00 295.85-239184.29 296.86 295.53 1.00 -1
> > 4 -1.00 308.17-239136.45 307.64 307.64 0.88 -1
> > 5 1.00 308.06-238988.58 309.01 310.44 0.31 -1
> > 6 1.00 305.13-239138.99 304.91 303.56 0.94 -1
> > 7 1.00 297.85-239308.56 295.53 296.86 1.00 -1
> > 8 1.00 301.01-239380.21 302.21 300.86 1.00 -1
> > 9 1.00 298.53-239203.29 298.19 299.52 0.94 -1
> > 10 -1.00 304.70-239232.45 306.27 306.27 0.88 -1
> > 11 1.00 302.69-239202.78 303.56 304.91 1.00 -1
> > 12 1.00 294.94-239499.66 294.21 292.90 1.00 -1
> > 13 1.00 300.69-239395.23 300.86 302.21 0.94 -1
> > 14 1.00 286.37-239695.11 286.38 285.09 1.00 -1
> > 15 1.00 291.36-239520.08 290.28 291.58 1.00 -1
> > 16 1.00 281.85-239685.86 281.25 279.98 1.00 -1
> > 17 1.00 286.91-239521.64 287.68 288.97 1.00 -1
> > 18 1.00 285.86-239469.74 285.09 286.38 1.00 -1
> > 19 1.00 291.53-239557.96 291.58 290.28 0.94 -1
> > 20 1.00 287.61-239612.47 288.97 287.68 1.00 -1
> > 21 1.00 295.50-239511.96 292.90 294.21 1.00 -1
> > 22 1.00 277.08-239728.20 277.46 278.73 1.00 -1
> > 23 1.00 281.02-239549.47 279.98 281.25 1.00 -1
> > 24 1.00 285.24-239811.81 283.81 282.53 1.00 -1
> > 25 1.00 280.54-239919.66 278.73 277.46 1.00 -1
> > 26 1.00 275.03-239906.59 276.21 274.96 1.00 -1
> > 27 -1.00 273.96-239787.93 273.71 273.71 0.88 -1
> > 28 1.00 271.41-239907.75 271.23 270.00 0.88 -1
> > 29 -1.00 272.49-239881.87 272.47 272.47 0.75 -1
> > 30 1.00 273.86-239793.13 274.96 276.21 1.00 -1
> > 31 1.00 270.74-239929.02 270.00 271.23 0.69 -1
> > 32 1.00 284.17-239559.23 282.53 283.81 1.00 -1
> > # exchange 33
> > 1 1.00 298.56-239647.71 298.19 296.86 0.91 -1
> > 2 1.00 310.32-239222.61 309.01 307.64 0.30 -1
> > 3 1.00 294.15-239565.38 295.53 294.21 0.97 -1
> > 4 1.00 303.38-239211.71 307.64 309.01 0.91 -1
> > 5 -1.00 311.39-239214.75 310.44 310.44 0.06 -1
> > 6 1.00 303.15-239587.23 303.56 302.21 0.97 -1
> > 7 1.00 295.82-239452.66 296.86 298.19 1.03 -1
> > 8 1.00 301.75-239706.01 300.86 299.52 0.91 -1
> > 9 1.00 299.23-239590.40 299.52 300.86 0.97 -1
> > 10 1.00 306.48-239596.64 306.27 304.91 0.85 -1
> > 11 1.00 304.11-239317.37 304.91 306.27 0.97 -1
> > 12 1.00 295.12-239733.48 292.90 291.58 0.97 -1
> > 13 1.00 302.37-239381.64 302.21 303.56 1.03 -1
> > 14 1.00 285.43-239993.86 285.09 283.81 0.97 -1
> > 15 1.00 293.03-239827.37 291.58 292.90 0.97 -1
> > 16 1.00 281.71-240076.80 279.98 278.73 0.97 -1
> > 17 1.00 287.46-239707.00 288.97 290.28 1.03 -1
> > 18 1.00 287.92-239662.53 286.38 287.68 1.03 -1
> > 19 1.00 289.38-239765.38 290.28 288.97 0.97 -1
> > 20 1.00 287.47-239790.23 287.68 286.38 0.97 -1
> > 21 1.00 293.81-239572.60 294.21 295.53 1.03 -1
> > 22 1.00 279.07-239939.90 278.73 279.98 1.03 -1
> > 23 1.00 279.45-239795.77 281.25 282.53 1.03 -1
> > 24 1.00 282.05-240026.98 282.53 281.25 0.97 -1
> > 25 1.00 280.62-240229.59 277.46 276.21 0.97 -1
> > 26 1.00 276.37-240004.49 274.96 273.71 0.97 -1
> > 27 1.00 274.39-240117.97 273.71 274.96 0.91 -1
> > 28 -1.00 271.27-240176.99 270.00 270.00 0.67 -1
> > 29 1.00 272.88-240227.77 272.47 271.23 0.73 -1
> > 30 1.00 277.02-240107.91 276.21 277.46 1.03 -1
> > 31 1.00 271.63-240007.57 271.23 272.47 0.91 -1
> > 32 1.00 283.63-239721.84 283.81 285.09 1.03 -1
> >
> > Temperatures were selected using: http://folding.bmc.uu.se/remd/
> > The temperatures are:
> > 270.00, 271.24, 272.48, 273.73, 274.98, 276.24, 277.50, 278.76, 280.04,
> > 281.31, 282.59, 283.87, 285.17, 286.46, 287.76, 289.06, 290.37, 291.68,
> > 293.00, 294.32, 295.65, 296.98, 298.32, 299.66, 301.01, 302.35, 303.71,
> > 305.07, 306.43, 307.81, 309.18, 310.57
> >
> > These temperatures are based on 102229 degrees of freedom for the system
> > and a desired exchange probability of .22. According to my mdout files,
> > the system actually has 101423 degrees of freedom. So I think the
> > temperatures may be a bit off, but I would be very surprised if they were
> > responsible for anything as drastically weird as what I'm seeing.
> >
> > Has anybody seen these types of results before? What was the the cause?
> > How did yo solve it?
> >
> > Christopher Thiebaut
> > Graduate Student
> > Purdue University
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------------------------------------------------------
Christina Bergonzo, PhD
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
30 South 2000 East, Rm. 201
Salt Lake City, UT 84112-5820
Office: L.S. Skaggs Pharmacy Research Institute, Rm.4290
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652 / Fax: (801) 585-6208
---------------------------------------------------------------------------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 6
Date: Mon, 7 Apr 2014 16:24:34 -0400
From: Lara rajam <lara.4884.gmail.com>
Subject: Re: [AMBER] antechamber
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAPQ+66Ait8WNwBRXhDWO5+FhuAA-SuqKdpK1i-2V_61bb=ke6A.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
I can understand the gaff parameters are in lower case , thanks you for
your suggestion
but still i am not able to build the parameter it says the error as below
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Could not find angle parameter: s6 - os - ca
Could not find angle parameter: c - ca - os
Could not find angle parameter: c - ca - cc
Could not find angle parameter: ca - os - s6
Could not find angle parameter: ca - cc - ca
Could not find angle parameter: os - ca - cc
Could not find angle parameter: ca - os - s6
Could not find angle parameter: ca - os - s6
Building proper torsion parameters.
** No torsion terms for ca-os-cc-ca
** No torsion terms for ca-os-cc-ca
** No torsion terms for os-cc-ca-c
** No torsion terms for os-cc-ca-os
** No torsion terms for os-cc-ca-ca
** No torsion terms for os-cc-ca-ca
** No torsion terms for c-ca-cc-ca
** No torsion terms for ca-cc-ca-ca
** No torsion terms for ca-cc-ca-ca
** No torsion terms for os-ca-cc-ca
Building improper torsion parameters.
total 6 improper torsions applied
How to fix these improper terms
thank you
On Mon, Apr 7, 2014 at 3:12 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Apr 07, 2014, Lara rajam wrote:
>
> > I was able to proceed with all the commands, but the topology file is
> not
> > generated
> >
> > I have the following error
>
> ....your snippet didn't show any errors, just warnings. But there must
> have
> been errors, so look carefully in the leap.log file.
>
> >
> > O -SO 0.00 0.000 ATTN, need revision
> > SO-OS 0.00 0.000 ATTN, need revision
>
> This looks odd, since the atom types are in upper case, but gaff atom types
> are always lower case. There is almost certainly something wrong with the
> structure, or with the ways in which antechamber is identifying atoms
> types:
> did you ask for "-at amber"? (don't do that, unless you know your molecule
> has just the sorts of functional groups found in proteins or nucleic
> acids.)
>
> ...good luck...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
------------------------------
Message: 7
Date: Mon, 7 Apr 2014 18:00:15 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] antechamber
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAEk9e3qnyAvE=cW6LPVh54JjKWe5_UZfCN5kyUEH5ktc3P4xog.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
On Mon, Apr 7, 2014 at 4:24 PM, Lara rajam <lara.4884.gmail.com> wrote:
> I can understand the gaff parameters are in lower case , thanks you for
> your suggestion
> but still i am not able to build the parameter it says the error as below
>
You didn't say what you actually did. Did you source leaprc.gaff? Did
you run parmchk to generate an frcmod file from the mol2 in order to fill
in missing parameters? Have you run this tutorial successfully:
http://ambermd.org/tutorials/basic/tutorial4b/ ?
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Could not find angle parameter: s6 - os - ca
> Could not find angle parameter: c - ca - os
> Could not find angle parameter: c - ca - cc
> Could not find angle parameter: ca - os - s6
> Could not find angle parameter: ca - cc - ca
> Could not find angle parameter: os - ca - cc
> Could not find angle parameter: ca - os - s6
> Could not find angle parameter: ca - os - s6
> Building proper torsion parameters.
> ** No torsion terms for ca-os-cc-ca
> ** No torsion terms for ca-os-cc-ca
> ** No torsion terms for os-cc-ca-c
> ** No torsion terms for os-cc-ca-os
> ** No torsion terms for os-cc-ca-ca
> ** No torsion terms for os-cc-ca-ca
> ** No torsion terms for c-ca-cc-ca
> ** No torsion terms for ca-cc-ca-ca
> ** No torsion terms for ca-cc-ca-ca
> ** No torsion terms for os-ca-cc-ca
> Building improper torsion parameters.
> total 6 improper torsions applied
>
> How to fix these improper terms
>
These are missing angles and dihedrals, NOT missing improper torsions.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
Message: 8
Date: Mon, 7 Apr 2014 20:04:52 -0500
From: Milo Westler <milo.nmrfam.wisc.edu>
Subject: [AMBER] REMD with pmemd.cuda
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CADRT24pNcBDLtQxZ2O9fQp-wwLbYECxK5A77gQEfoPNMa3b-eQ.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Anyone know of a recent tutorial to do temperature REMD on multiple gpus?
Thanks,
--
-- Milo
===================================================
National Magnetic Resonance Facility at Madison
An NIH-Supported Resource Center
W. Milo Westler, Ph.D.
NMRFAM Director
Senior Scientist
and
Adjunct Professor
Department of Biochemistry
University of Wisconsin-Madison
433 Babcock Drive
Madison, WI USA 53706-1544
EMAIL: milo.nmrfam.wisc.edu
PHONE: (608)-263-9599
FAX: (608)-263-1722
=======================================================================
========
------------------------------
Message: 9
Date: Mon, 7 Apr 2014 19:33:01 -0700 (PDT)
From: Jio M <jiomm.yahoo.com>
Subject: [AMBER] number of ions (integral) too much in RDF plot
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<1396924381.77882.YahooMailNeo.web120801.mail.ne1.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1
Hi All
I am using radial function to plot RDF of K ions around center of mass of O atoms. I have around 2100 K+ ions and octahedron box (149.1524703 149.1524703 149.1524703)
radial temp.dat 0.1 95 :K+ :1-389.O volume intrdf temp_int.dat
I should get almost exact number of K+ in my box after integrating. I have following queries:
1) The integral values goes upto?1076448?which is too high. Also what should be max bin size in this case to get expected number of ions? I have chosen 95 because the RDF plot shows fall at 95 Angstroms (also it confuses me as box size dimension goes upto 149 Angstroms and I should see a fall around 140 or so)
2) Also I have one more query regarding 'volume' key word used here. In manual it says??
"..?if the volume? keyword is specified the density is determined from the?average volume of the system over all Frames."?
So in this case does this mean density is a 'number density' which is = (total number of K+ ions in a box / avg. volume of box)
thanks
JIom
------------------------------
Message: 10
Date: Tue, 8 Apr 2014 11:43:54 +0800
From: Yeng-Tseng Wang <c00jsw00.gmail.com>
Subject: [AMBER] About the error "Unable to correctly identify element
CU" in QMMM simulation
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAPdDpjBHK4g_yfE8nfEp0shCsX55Lh_6Cy-ZmjVu48Gqbuhn_g.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear all,
I used the amber 12/ gaussian09 to study a enzyme with the two
cofators(Cu). But the error occured. Could you tell me how to modify the
related code ? I have looked for the related information (
http://archive.ambermd.org/200910/0346.html), but I can't find the code "
*qmmm_module.f*" in amber 12.
Thanks for your help
Yeng-Tseng (Phil) Wang
------------------------------
Message: 11
Date: Tue, 8 Apr 2014 14:34:26 +0900
From: KangMooseok <weirdwitch13.hotmail.com>
Subject: [AMBER] When I run the pmemd.cuda, sometimes computer will be
rebooted.
To: "amber.ambermd.org" <amber.ambermd.org>
Message-ID: <BAY169-W6766C23EC87C04D9F3DBA0C16B0.phx.gbl>
Content-Type: text/plain; charset="ks_c_5601-1987"
Dear amber users. When I run pmemd.cuda, sometimes computer will be rebooted automatically, without error message. Normally the mdout file shows the gpu information. But in this case mdout files do not show the gpu information. And hang then after automatically rebooted. It happens randomly in each 105 nodes. What is the problem? Is it unknown bug, or hardware problem?
My system isE5-2650v2, GTX titan.CentOS 6.4, Intel compiler 14.0.0.080, cuda5.5 (Nvidia driver 334.21)amberTools13 bugfix.22, amber12 bugfix.21
Thanks and regards. Mooseok Kang
normal mdout : ------------------------------------------------------- Amber 12 SANDER 2012 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 12 | Run on 04/04/2014 at 20:37:03 [-O]verwriting output File Assignments:| MDIN: ../md_shake.in| MDOUT: md571.out| INPCRD: mth_md570.rst| PARM: ../mth_WAT.top| RESTRT: mth_md571.rst| REFC: refc| MDVEL: mdvel| MDEN: mden| MDCRD: mdcrd| MDINFO: mth_md571.info Here is the input file: MD, NPT, 300 K &cntrl imin = 0, irest = 1, ntx = 5, nstlim = 50000, dt = 0.002, ntt = 3, ntb = 2, ntp = 1, gamma_ln=1.0, temp0 = 300.0, pres0 = 1.0, taup = 2.0, ntc = 2, ntf = 2, cut = 9.0, ioutfm = 1, iwrap = 1, ntwx = 5000, ntwr = 5000, ntpr = 5000 / |--------------------- INFORMATION ----------------------| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.| Version 12.3.1|| 08/07/2013|| Implementation by:| Ross C. Walker (SDSC)| Scott Le Grand (nVIDIA)| Duncan Poole (nVIDIA)|| CAUTION: The CUDA code is currently experimental.| You use it at your own risk. Be sure to| check ALL results carefully.|| Precision model in use:| [SPFP] - Mixed Single/Double/Fixed Point Precision.| (Default)||-------------------------------------------------------- |----------------- CITATION INFORMATION -----------------|| When publishing work that utilized the CUDA version| of AMBER, please cite the following in addition to| the regular AMBER citations:|| - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan| Poole; Scott Le Grand; Ross C. Walker "Routine| microsecond molecular dynamics simulations with| AMBER - Part II: Particle Mesh Ewald", J. Chem.| Theory Comput., 2013, DOI: 10.1021/ct400314y. adnormal mdout ------------------------------------------------------- Amber 12 SANDER 2012 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 12 | Run on 04/04/2014 at 20:40:36 [-O]verwriting output File Assignments:| MDIN: ../md_shake.in| MDOUT: md572.out| INPCRD: mth_md571.rst| PARM: ../mth_WAT.top| RESTRT: mth_md572.rst| REFC: refc| MDVEL: mdvel| MDEN: mden| MDCRD: mdcrd| MDINFO: mth_md572.info Here is the input file: MD, NPT, 300 K &cntrl imin = 0, irest = 1, ntx = 5, nstlim = 50000, dt = 0.002, ntt = 3, ntb = 2, ntp = 1, gamma_ln=1.0, temp0 = 300.0, pres0 = 1.0, taup = 2.0, ntc = 2, ntf = 2, cut = 9.0, ioutfm = 1, iwrap = 1, ntwx = 5000, ntwr = 5000, ntpr = 5000 /
------------------------------
Message: 12
Date: Tue, 8 Apr 2014 11:28:18 +0530
From: Arunima Shilpi <writetoash28.gmail.com>
Subject: [AMBER] error in reading protein file
To: amber.ambermd.org
Message-ID:
<CAM90emZHDBjWmRF0Uf7_LAqMttu34YOStsCFBDY943wKedzFCQ.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear Sir
Presently I am studying protein-ligand interaction in which one of the
residue along the active site have been mutated to ILE . Now when I load
the protein in tleap it shows the following error
complex=loadpdb C1191I_ZINC7271_min.pdb
Loading PDB file: ./C1191I_ZINC7271_min.pdb
Created a new atom named: CD within residue: .R<ILE 709>
Added missing heavy atom: .R<ILE 709>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 731>
Added missing heavy atom: .R<ILE 731>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 752>
Added missing heavy atom: .R<ILE 752>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 766>
Added missing heavy atom: .R<ILE 766>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 828>
Added missing heavy atom: .R<ILE 828>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 835>
Added missing heavy atom: .R<ILE 835>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 899>
Added missing heavy atom: .R<ILE 899>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 923>
Added missing heavy atom: .R<ILE 923>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 942>
Added missing heavy atom: .R<ILE 942>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 974>
Added missing heavy atom: .R<ILE 974>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 977>
Added missing heavy atom: .R<ILE 977>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 980>
Added missing heavy atom: .R<ILE 980>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 995>
Added missing heavy atom: .R<ILE 995>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 997>
Added missing heavy atom: .R<ILE 997>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1020>
Added missing heavy atom: .R<ILE 1020>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1114>
Added missing heavy atom: .R<ILE 1114>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1121>
Added missing heavy atom: .R<ILE 1121>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1145>
Added missing heavy atom: .R<ILE 1145>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1147>
Added missing heavy atom: .R<ILE 1147>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1268>
Added missing heavy atom: .R<ILE 1268>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1269>
Added missing heavy atom: .R<ILE 1269>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1308>
Added missing heavy atom: .R<ILE 1308>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1319>
Added missing heavy atom: .R<ILE 1319>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1340>
Added missing heavy atom: .R<ILE 1340>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1362>
Added missing heavy atom: .R<ILE 1362>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1367>
Added missing heavy atom: .R<ILE 1367>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1382>
Added missing heavy atom: .R<ILE 1382>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1396>
Added missing heavy atom: .R<ILE 1396>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1446>
Added missing heavy atom: .R<ILE 1446>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1519>
Added missing heavy atom: .R<ILE 1519>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1538>
Added missing heavy atom: .R<ILE 1538>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1542>
Added missing heavy atom: .R<ILE 1542>.A<CD1 14>
Added missing heavy atom: .R<CALA 1550>.A<OXT 11>
total atoms in file: 7224
Leap added 7130 missing atoms according to residue templates:
33 Heavy
7097 H / lone pairs
The file contained 32 atoms not in residue templates
I request you to kindly guide me rectifying the above error.
Regards
Arunima
------------------------------
Message: 13
Date: Tue, 8 Apr 2014 15:01:45 +0900
From: KangMooseok <weirdwitch13.hotmail.com>
Subject: [AMBER] When I run the pmemd.cuda, sometimes computer will be
rebooted.??
To: "amber.ambermd.org" <amber.ambermd.org>
Message-ID: <BAY169-W826767356FA886422FCE5EC16B0.phx.gbl>
Content-Type: text/plain; charset="windows-1256"
Dear amber users.
When I run pmemd.cuda, sometimes computer will be rebooted automatically, without error message.
Normally the mdout file shows the gpu information. But in this case mdout files do not show the gpu information. And hang then after automatically rebooted. It happens randomly in each 105 nodes.What is the problem? Is it unknown bug, or hardware problem?
My system isE5-2650v2, GTX titan.CentOS 6.4, Intel compiler 14.0.0.080, cuda5.5 (Nvidia driver 334.21)amberTools13 bugfix.22, amber12 bugfix.21
Thanks and regards.
Mooseok Kang
normal mdout file:
-------------------------------------------------------Amber 12 SANDER 2012------------------------------------------------------- | PMEMD implementation of SANDER, Release 12 | Run on 04/04/2014 at 20:37:03 [-O]verwriting output File Assignments:| MDIN: ../md_shake.in| MDOUT: md571.out| INPCRD: mth_md570.rst| PARM: ../mth_WAT.top| RESTRT: mth_md571.rst| REFC: refc| MDVEL: mdvel| MDEN: mden| MDCRD: mdcrd| MDINFO: mth_md571.info Here is the input file: MD, NPT, 300 K&cntrlimin = 0, irest = 1, ntx = 5,nstlim = 50000, dt = 0.002,ntt = 3, ntb = 2, ntp = 1, gamma_ln=1.0,temp0 = 300.0, pres0 = 1.0, taup = 2.0,ntc = 2, ntf = 2,cut = 9.0, ioutfm = 1, iwrap = 1,ntwx = 5000, ntwr = 5000, ntpr = 5000/ |--------------------- INFORMATION ----------------------| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.| Version 12.3.1|| 08/07/2013|| Implementation by:| Ross C. Walker (SDSC)| Scott Le Grand (nVIDIA)| Duncan Poole (nVIDIA)|| CAUTION: The CUDA code is currently experimental.| You use it at your own risk. Be sure to| check ALL results carefully.|| Precision model in use:| [SPFP] - Mixed Single/Double/Fixed Point Precision.| (Default)||-------------------------------------------------------- |----------------- CITATION INFORMATION -----------------|| When publishing work that utilized the CUDA version| of AMBER, please cite the following in addition to| the regular AMBER citations:|| - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan| Poole; Scott Le Grand; Ross C. Walker "Routine| microsecond molecular dynamics simulations with| AMBER - Part II: Particle Mesh Ewald", J. Chem.| Theory Comput., 2013, DOI: 10.1021/ct400314y.
abnormal mdout file: -------------------------------------------------------Amber 12 SANDER 2012------------------------------------------------------- | PMEMD implementation of SANDER, Release 12 | Run on 04/04/2014 at 20:40:36 [-O]verwriting output File Assignments:| MDIN: ../md_shake.in| MDOUT: md572.out| INPCRD: mth_md571.rst| PARM: ../mth_WAT.top| RESTRT: mth_md572.rst| REFC: refc| MDVEL: mdvel| MDEN: mden| MDCRD: mdcrd| MDINFO: mth_md572.info Here is the input file: MD, NPT, 300 K&cntrlimin = 0, irest = 1, ntx = 5,nstlim = 50000, dt = 0.002,ntt = 3, ntb = 2, ntp = 1, gamma_ln=1.0,temp0 = 300.0, pres0 = 1.0, taup = 2.0,ntc = 2, ntf = 2,cut = 9.0, ioutfm = 1, iwrap = 1,ntwx = 5000, ntwr = 5000, ntpr = 5000/
------------------------------
Message: 14
Date: Tue, 8 Apr 2014 11:35:11 +0530
From: Arunima Shilpi <writetoash28.gmail.com>
Subject: [AMBER] error in loading protein
To: amber.ambermd.org
Message-ID:
<CAM90emYxtgG9mxC8g4y6G0xLg9=RSjypvOYXROACaQmR+8v5qw.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear sir
Presently I am studying Protein-Ligand interaction in which one of the
resuide has been mutated to ILE. While saving the co-ordinates it shows the
following error
FATAL: Atom .R<ILE 709>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 731>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 752>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 766>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 828>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 835>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 899>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 923>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 942>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 974>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 977>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 980>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 995>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 997>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 1020>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 1114>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 1121>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 1145>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 1147>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 1268>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 1269>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 1308>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 1319>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 1340>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 1362>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 1367>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 1382>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 1396>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 1446>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 1519>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 1538>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 1542>.A<CD 20> does not have a type.
Failed to generate parameters
Parameter file was not saved.
I request you to kindly guide me in debugging the error
Regards
Arunima
------------------------------
Message: 15
Date: Tue, 8 Apr 2014 09:20:18 +0200
From: Soumendranath Bhakat <bhakatsoumendranath.gmail.com>
Subject: Re: [AMBER] error in loading protein
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CACF5EqkqJwEBDcJiL+hUN0OmdH7cnYeDtCoepSPurBHB+CO_LQ.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hii;
This seems to be an issue with isoleucine. Try deleting all hydrogens from
those residues. You can use reduce, trim option to do that. Leap will
automatically add them back.
I think the problem is that Leap doesn't find CD 20 as atom from its amino
acid library. You can try to check the amino acid library located at
$AMBERHOME/dat/leap/lib/all_amino94.lib
Modify accordingly if you can or try from scratch. Sometimes leap unable to
map the amino acids because of bad type such as CD 20 CG 20 etc.
Try deleting all hydrogens from the receptor using Chimera, Reduce or any
other programme and re run the leap again.
All d best.
On Tue, Apr 8, 2014 at 8:05 AM, Arunima Shilpi <writetoash28.gmail.com>wrote:
> Dear sir
>
> Presently I am studying Protein-Ligand interaction in which one of the
> resuide has been mutated to ILE. While saving the co-ordinates it shows the
> following error
>
> FATAL: Atom .R<ILE 709>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 731>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 752>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 766>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 828>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 835>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 899>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 923>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 942>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 974>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 977>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 980>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 995>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 997>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1020>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1114>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1121>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1145>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1147>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1268>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1269>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1308>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1319>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1340>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1362>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1367>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1382>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1396>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1446>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1519>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1538>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1542>.A<CD 20> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
> I request you to kindly guide me in debugging the error
>
> Regards
>
> Arunima
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks & Regards;
Soumendranath Bhakat
------------------------------
Message: 16
Date: Tue, 8 Apr 2014 03:37:29 -0400
From: Nhai <nhai.qn.gmail.com>
Subject: Re: [AMBER] REMD with pmemd.cuda
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <956C381A-2CA5-4BAE-9791-286E890F25FC.gmail.com>
Content-Type: text/plain; charset=us-ascii
I dont think there is any difference.
Hai Nguyen
> On Apr 7, 2014, at 9:04 PM, Milo Westler <milo.nmrfam.wisc.edu> wrote:
>
> Anyone know of a recent tutorial to do temperature REMD on multiple gpus?
>
> Thanks,
>
> --
> -- Milo
> ===================================================
> National Magnetic Resonance Facility at Madison
> An NIH-Supported Resource Center
>
> W. Milo Westler, Ph.D.
>
> NMRFAM Director
> Senior Scientist
> and
> Adjunct Professor
> Department of Biochemistry
> University of Wisconsin-Madison
> 433 Babcock Drive
> Madison, WI USA 53706-1544
> EMAIL: milo.nmrfam.wisc.edu
> PHONE: (608)-263-9599
> FAX: (608)-263-1722
> =======================================================================
> ========
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 17
Date: Tue, 8 Apr 2014 17:32:39 +0800
From: Neha Gandhi <n.gandhiau.gmail.com>
Subject: [AMBER] Karplus J-coupling
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CA+Hq8HwvjrxPnx34K2haW-G68GC6ByynoVvt_xCduLLhXELmyg.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear List,
Ptraj/Cpptraj has J-coupling function and Karplus.txt consists of constants
for side-chain torsions (around CA-CB atoms). Is there a way to calculate
J-coupling round the backbone torsion phi? If somebody can direct me to a
paper with relevant values, I might be able to edit the Karplus.txt file.
My question might be somewhat irrelevant for AMBER mailing list. However,
if anybody has done such analyses your feedback is appreciated.
--
Regards,
Dr. Neha S. Gandhi,
Curtin Research Fellow,
School of Biomedical Sciences,
Curtin University,
Perth GPO U1987
Australia
LinkedIn
Research Gate
------------------------------
Message: 18
Date: Tue, 08 Apr 2014 07:29:14 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] About the error "Unable to correctly identify
element CU" in QMMM simulation
To: amber.ambermd.org
Message-ID: <1396956554.4240.11.camel.heroes-out.rutgers.edu>
Content-Type: text/plain; charset="UTF-8"
On Tue, 2014-04-08 at 11:43 +0800, Yeng-Tseng Wang wrote:
> Dear all,
> I used the amber 12/ gaussian09 to study a enzyme with the two
> cofators(Cu). But the error occured. Could you tell me how to modify the
> related code ? I have looked for the related information (
> http://archive.ambermd.org/200910/0346.html), but I can't find the code "
> *qmmm_module.f*" in amber 12.
It is qmmm_module.F90 in AmberTools 12 and 13.
($AMBERHOME/AmberTools/src/sqm/qmmm_module.F90). Note that Copper is
already recognized, but that element recognition is done based on the
first letter of the atom name and the atomic mass. In particular,
Copper must have its first letter be a C (not a space) and it must have
a mass between 61 and 65 Amu.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
Message: 19
Date: Tue, 08 Apr 2014 07:35:45 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] When I run the pmemd.cuda, sometimes computer
will be rebooted.
To: amber.ambermd.org
Message-ID: <1396956945.4240.17.camel.heroes-out.rutgers.edu>
Content-Type: text/plain; charset="UTF-8"
On Tue, 2014-04-08 at 14:34 +0900, KangMooseok wrote:
> Dear amber users. When I run pmemd.cuda, sometimes computer will
> be rebooted automatically, without error message. Normally the mdout
> file shows the gpu information. But in this case mdout files do not
> show the gpu information. And hang then after automatically rebooted.
> It happens randomly in each 105 nodes. What is the problem? Is it
> unknown bug,
It is _definitely_ not an Amber bug. Maybe a driver bug. Maybe a
kernel bug. Maybe buggy hardware. FWIW, I've been using Nvidia driver
334.21 for awhile on my machine with no problems.
Does it happen to _every_ node? If so, try downgrading the Nvidia
driver (maybe to one of the stable drivers in the 331 line). If it only
happens to a small subset of the nodes, look into the possibility of a
hardware problem.
HTH,
Jason
P.S. Your entire email came crammed on 2 lines (for me). That makes it
VERY hard to understand your mdout file since the formatting is
completely messed up. Please try to make sure your emails are formatted
correctly in the future so we can make more sense of whatever output you
paste there.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
Message: 20
Date: Tue, 08 Apr 2014 07:42:09 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] error in reading protein file
To: amber.ambermd.org
Message-ID: <1396957329.4240.23.camel.heroes-out.rutgers.edu>
Content-Type: text/plain; charset="UTF-8"
On Tue, 2014-04-08 at 11:28 +0530, Arunima Shilpi wrote:
> Dear Sir
>
>
> Presently I am studying protein-ligand interaction in which one of the
> residue along the active site have been mutated to ILE . Now when I load
> the protein in tleap it shows the following error
>
> complex=loadpdb C1191I_ZINC7271_min.pdb
> Loading PDB file: ./C1191I_ZINC7271_min.pdb
> Created a new atom named: CD within residue: .R<ILE 709>
> Added missing heavy atom: .R<ILE 709>.A<CD1 14>
> Created a new atom named: CD within residue: .R<ILE 731>
> Added missing heavy atom: .R<ILE 731>.A<CD1 14>
> Created a new atom named: CD within residue: .R<ILE 752>
> Added missing heavy atom: .R<ILE 752>.A<CD1 14>
All of your isoleucine residues have an atom named 'CD' in them in your
PDB file. The way tleap works is it matches the residues in your input
structure to the residue libraries that have been loaded before. That
is how it knows what connectivity and atom types to assign to all of the
atoms in each of the residues. A caveat of that approach is that all of
the atom names in your input structure must match _exactly_ the atom
names of the corresponding atoms in the LEaP library files. Any atom
that is _not_ in the input structure but is in the library file is
automatically added by LEaP.
This message states that a new atom was added to the residue (CD) which
was not in the template. Right after that, it says that LEaP adds a
missing atom CD1. This happens because the ILE residue in the Amber
library files name the delta-carbon in isoleucine CD1, but your PDB has
it named CD. If you change the names of CD to CD1 in your input PDB
file, this error will go away.
As a side-note, the atom names in Amber's library files are set to the
names used by the latest version of the PDB standard. So any PDB you
download today should work with the existing names (unless of course you
have a non-standard residue that has not yet been parametrized).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
Message: 21
Date: Tue, 08 Apr 2014 07:45:18 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] REMD with pmemd.cuda
To: amber.ambermd.org
Message-ID: <1396957518.4240.25.camel.heroes-out.rutgers.edu>
Content-Type: text/plain; charset="UTF-8"
On Tue, 2014-04-08 at 03:37 -0400, Nhai wrote:
> I dont think there is any difference.
Except of course you need to use pmemd.cuda.MPI instead of sander.MPI as
described in the relevant tutorial
[
http://ambermd.org/tutorials/advanced/tutorial7/] ;).
>
> Hai Nguyen
>
> > On Apr 7, 2014, at 9:04 PM, Milo Westler <milo.nmrfam.wisc.edu> wrote:
> >
> > Anyone know of a recent tutorial to do temperature REMD on multiple gpus?
> >
> > Thanks,
> >
> > --
> > -- Milo
> > ===================================================
> > National Magnetic Resonance Facility at Madison
> > An NIH-Supported Resource Center
> >
> > W. Milo Westler, Ph.D.
> >
> > NMRFAM Director
> > Senior Scientist
> > and
> > Adjunct Professor
> > Department of Biochemistry
> > University of Wisconsin-Madison
> > 433 Babcock Drive
> > Madison, WI USA 53706-1544
> > EMAIL: milo.nmrfam.wisc.edu
> > PHONE: (608)-263-9599
> > FAX: (608)-263-1722
> > =======================================================================
> > ========
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
Message: 22
Date: Tue, 8 Apr 2014 17:24:23 +0530
From: Ashutosh Shandilya <izerokelvin.gmail.com>
Subject: Re: [AMBER] REMD with pmemd.cuda
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAEwuNu-3NosiQwrZQTFD96H+NSd_X4zeRFLCL8UOFssYxRYNMQ.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
If we want to run eight replicas do we need eight cards? Can I run jobs on
two cards with eight replicas?
Thanks
On 8 April 2014 17:15, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, 2014-04-08 at 03:37 -0400, Nhai wrote:
> > I dont think there is any difference.
>
> Except of course you need to use pmemd.cuda.MPI instead of sander.MPI as
> described in the relevant tutorial
> [http://ambermd.org/tutorials/advanced/tutorial7/] ;).
>
>
> >
> > Hai Nguyen
> >
> > > On Apr 7, 2014, at 9:04 PM, Milo Westler <milo.nmrfam.wisc.edu> wrote:
> > >
> > > Anyone know of a recent tutorial to do temperature REMD on multiple
> gpus?
> > >
> > > Thanks,
> > >
> > > --
> > > -- Milo
> > > ===================================================
> > > National Magnetic Resonance Facility at Madison
> > > An NIH-Supported Resource Center
> > >
> > > W. Milo Westler, Ph.D.
> > >
> > > NMRFAM Director
> > > Senior Scientist
> > > and
> > > Adjunct Professor
> > > Department of Biochemistry
> > > University of Wisconsin-Madison
> > > 433 Babcock Drive
> > > Madison, WI USA 53706-1544
> > > EMAIL: milo.nmrfam.wisc.edu
> > > PHONE: (608)-263-9599
> > > FAX: (608)-263-1722
> > > =======================================================================
> > > ========
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
------------------------------
Message: 23
Date: Tue, 8 Apr 2014 08:24:27 -0400
From: David A Case <case.biomaps.rutgers.edu>
Subject: Re: [AMBER] Karplus J-coupling
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20140408122427.GF65485.biomaps.rutgers.edu>
Content-Type: text/plain; charset=iso-8859-1
On Tue, Apr 08, 2014, Neha Gandhi wrote:
>
> Ptraj/Cpptraj has J-coupling function and Karplus.txt consists of constants
> for side-chain torsions (around CA-CB atoms). Is there a way to calculate
> J-coupling round the backbone torsion phi? If somebody can direct me to a
> paper with relevant values, I might be able to edit the Karplus.txt file.
It's not recent, but the paper below has suggested Karplus fits for all six
3-bond J couplings about the phi angle. I'm sure things haven't changed very
much, but a citation search on this might reveal more recent fits.
..regards...dac
%A D.A. Case
%A C. Scheurer
%A R. Br?schweiler
%T Static and Dynamic Effects on Vicinal Scalar J Couplings in Proteins
and Peptides: A MD/DFT Analysis
%J J. Am. Chem. Soc.
%V 122
%P 10390-10397
%D 2000
------------------------------
Message: 24
Date: Tue, 8 Apr 2014 08:40:55 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] REMD with pmemd.cuda
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAEk9e3odttGb1kEgSkMi+fcVehBo7CAxC83vs8EhzfOFYUW6zg.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
On Tue, Apr 8, 2014 at 7:54 AM, Ashutosh Shandilya <izerokelvin.gmail.com>wrote:
> If we want to run eight replicas do we need eight cards? Can I run jobs on
> two cards with eight replicas?
>
It may be possible to run multiple replicas per card, but it's strongly
recommended to have a separate GPU for each replica. Performance will
severely suffer otherwise.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
Message: 25
Date: Tue, 8 Apr 2014 05:44:35 -0700 (PDT)
From: Jio M <jiomm.yahoo.com>
Subject: [AMBER] number of ions (integral) too much in RDF plot
To: amber <amber.ambermd.org>
Message-ID:
<1396961075.9789.YahooMailNeo.web120806.mail.ne1.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1
Hi All
{Sorry if posted twice as I am not getting confirmation copy mail}
I am using radial function to plot RDF of K ions around center of mass of O atoms. I have around 2100 K+ ions and octahedron box (149.1524703 149.1524703 149.1524703)
radial temp.dat 0.1 95 :K+ :1-389.O volume intrdf temp_int.dat
I should get almost exact number of K+ in my box after integrating. I have following queries:
1) The integral values goes upto?1076448?which is too high. Also what should be max bin size in this case to get expected number of ions? I have chosen 95 because the RDF plot shows fall at 95 Angstroms (also it confuses me as box size dimension goes upto 149 Angstroms and I should see a fall around 140 or so)
2) Also I have one more query regarding 'volume' key word used here. In manual it says??
"..?if the volume? keyword is specified the density is determined from the?average volume of the system over all Frames."?
So in this case does this mean density is a 'number density' which is = (total number of K+ ions in a box / avg. volume of box)
thanks
JIom
------------------------------
Message: 26
Date: Tue, 8 Apr 2014 18:15:09 +0530
From: Ashutosh Shandilya <izerokelvin.gmail.com>
Subject: Re: [AMBER] REMD with pmemd.cuda
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAEwuNu9qeq=X4D4O1Rdf-=iGOMiCOfVphFGUug+AHUiOZQZwaA.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
If we want to run eight replicas do we need eight cards? Can I run jobs on
two cards with eight replicas?
Would there be any memory issues etc.
Thanks
On 8 April 2014 17:24, Ashutosh Shandilya <izerokelvin.gmail.com> wrote:
> If we want to run eight replicas do we need eight cards? Can I run jobs on
> two cards with eight replicas?
>
> Thanks
>
>
> On 8 April 2014 17:15, Jason Swails <jason.swails.gmail.com> wrote:
>
>> On Tue, 2014-04-08 at 03:37 -0400, Nhai wrote:
>> > I dont think there is any difference.
>>
>> Except of course you need to use pmemd.cuda.MPI instead of sander.MPI as
>> described in the relevant tutorial
>> [http://ambermd.org/tutorials/advanced/tutorial7/] ;).
>>
>>
>> >
>> > Hai Nguyen
>> >
>> > > On Apr 7, 2014, at 9:04 PM, Milo Westler <milo.nmrfam.wisc.edu>
>> wrote:
>> > >
>> > > Anyone know of a recent tutorial to do temperature REMD on multiple
>> gpus?
>> > >
>> > > Thanks,
>> > >
>> > > --
>> > > -- Milo
>> > > ===================================================
>> > > National Magnetic Resonance Facility at Madison
>> > > An NIH-Supported Resource Center
>> > >
>> > > W. Milo Westler, Ph.D.
>> > >
>> > > NMRFAM Director
>> > > Senior Scientist
>> > > and
>> > > Adjunct Professor
>> > > Department of Biochemistry
>> > > University of Wisconsin-Madison
>> > > 433 Babcock Drive
>> > > Madison, WI USA 53706-1544
>> > > EMAIL: milo.nmrfam.wisc.edu
>> > > PHONE: (608)-263-9599
>> > > FAX: (608)-263-1722
>> > >
>> =======================================================================
>> > > ========
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
------------------------------
Message: 27
Date: Tue, 8 Apr 2014 14:57:58 +0200
From: "Urszula Uciechowska" <urszula.uciechowska.biotech.ug.edu.pl>
Subject: [AMBER] error in input file /nmropt=1
To: "AMBER Mailing List" <amber.ambermd.org>
Message-ID:
<df113a0ca70d9af6f9a62890a9b5ce37.squirrel.poczta.ug.edu.pl>
Content-Type: text/plain;charset=utf-8
Dear AMBER users,
I'm trying to do some MD with sander.MPI and distance restraints (nmropt=1)
in AMBER 11.
No matter how I write the restraints I always get the same message:
Flags:
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 42.653
My input file:
Heating
&cntrl
imin = 0,
irest = 0,
ntx = 1,
cut = 9,
ntb = 1,
iwrap = 1,
nmropt = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 125000, dt = 0.002,
ntpr = 100, ntwx = 500, ntwr = 1000,
&end
/
&wt TYPE='END'
DISANG=dist.RST
LISTOUT=dist.out
/
&end
please guide me!
thanks.
Urszula
-----------------------------------------
Ta wiadomo?? zosta?a wys?ana z serwera Uniwersytetu Gda?skiego
http://www.ug.edu.pl/
------------------------------
Message: 28
Date: Tue, 8 Apr 2014 09:03:31 -0400
From: Asaminew Haile <ashaethio.gmail.com>
Subject: Re: [AMBER] error in input file /nmropt=1
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <EB12A462-3E9B-4796-A90A-CDDAE3CA2297.gmail.com>
Content-Type: text/plain; charset=utf-8
On Apr 8, 2014, at 8:57 AM, Urszula Uciechowska <urszula.uciechowska.biotech.ug.edu.pl> wrote:
> Dear AMBER users,
> I'm trying to do some MD with sander.MPI and distance restraints (nmropt=1)
> in AMBER 11.
> No matter how I write the restraints I always get the same message:
>
> Flags:
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
>
> | peek_ewald_inpcrd: Box info found
> |Largest sphere to fit in unit cell has radius = 42.653
>
>
> My input file:
> Heating
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> cut = 9,
> ntb = 1,
> iwrap = 1,
> nmropt = 1,
> ntc = 2,
> ntf = 2,
> tempi = 0.0,
> temp0 = 300.0,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 125000, dt = 0.002,
> ntpr = 100, ntwx = 500, ntwr = 1000,
> &end
> /
> &wt TYPE='END'
> DISANG=dist.RST
Can you post your dist.RST file?
> LISTOUT=dist.out
> /
> &end
>
> please guide me!
>
> thanks.
> Urszula
>
>
>
> -----------------------------------------
> Ta wiadomo?? zosta?a wys?ana z serwera Uniwersytetu Gda?skiego
> http://www.ug.edu.pl/
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 29
Date: Tue, 8 Apr 2014 15:12:56 +0200
From: "Urszula Uciechowska" <urszula.uciechowska.biotech.ug.edu.pl>
Subject: Re: [AMBER] error in input file /nmropt=1 with dist.RST
To: "AMBER Mailing List" <amber.ambermd.org>
Message-ID:
<66e10d6c9139d4f95b9ca033ad49bd8a.squirrel.poczta.ug.edu.pl>
Content-Type: text/plain;charset=utf-8
My dist.RST file:
&rst iat=3457,4153
r1=0,r2=13.8,r3=13.8,r4=100.0,rk2=10.0,rk3=10.0, /
&end
/Urszula
> On Apr 8, 2014, at 8:57 AM, Urszula Uciechowska
> <urszula.uciechowska.biotech.ug.edu.pl> wrote:
>
>> Dear AMBER users,
>> I'm trying to do some MD with sander.MPI and distance restraints
>> (nmropt=1)
>> in AMBER 11.
>> No matter how I write the restraints I always get the same message:
>>
>> Flags:
>> getting new box info from bottom of inpcrd
>> | INFO: Old style inpcrd file read
>>
>> | peek_ewald_inpcrd: Box info found
>> |Largest sphere to fit in unit cell has radius = 42.653
>>
>>
>> My input file:
>> Heating
>> &cntrl
>> imin = 0,
>> irest = 0,
>> ntx = 1,
>> cut = 9,
>> ntb = 1,
>> iwrap = 1,
>> nmropt = 1,
>> ntc = 2,
>> ntf = 2,
>> tempi = 0.0,
>> temp0 = 300.0,
>> ntt = 3,
>> gamma_ln = 1.0,
>> nstlim = 125000, dt = 0.002,
>> ntpr = 100, ntwx = 500, ntwr = 1000,
>> &end
>> /
>> &wt TYPE='END'
>> DISANG=dist.RST
> Can you post your dist.RST file?
>> LISTOUT=dist.out
>> /
>> &end
>>
>> please guide me!
>>
>> thanks.
>> Urszula
>>
>>
>>
>> -----------------------------------------
>> Ta wiadomo?? zosta?a wys?ana z serwera Uniwersytetu Gda?skiego
>> http://www.ug.edu.pl/
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
-----------------------------------------
Ta wiadomo?? zosta?a wys?ana z serwera Uniwersytetu Gda?skiego
http://www.ug.edu.pl/
------------------------------
Message: 30
Date: Tue, 8 Apr 2014 15:31:41 +0200
From: "Urszula Uciechowska" <urszula.uciechowska.biotech.ug.edu.pl>
Subject: Re: [AMBER] error in input file /nmropt=1 with dist.RST
To: "AMBER Mailing List" <amber.ambermd.org>
Message-ID:
<f4a415a2f149ea5beddcbfca78433c07.squirrel.poczta.ug.edu.pl>
Content-Type: text/plain;charset=utf-8
My dist.RST file:
&rst iat=3457,4153
r1=0,r2=13.8,r3=13.8,r4=100.0,rk2=10.0,rk3=10.0, /
&end
/Urszula
>
>> On Apr 8, 2014, at 8:57 AM, Urszula Uciechowska
>> <urszula.uciechowska.biotech.ug.edu.pl> wrote:
>>
>>> Dear AMBER users,
>>> I'm trying to do some MD with sander.MPI and distance restraints
>>> (nmropt=1)
>>> in AMBER 11.
>>> No matter how I write the restraints I always get the same message:
>>>
>>> Flags:
>>> getting new box info from bottom of inpcrd
>>> | INFO: Old style inpcrd file read
>>>
>>> | peek_ewald_inpcrd: Box info found
>>> |Largest sphere to fit in unit cell has radius = 42.653
>>>
>>>
>>> My input file:
>>> Heating
>>> &cntrl
>>> imin = 0,
>>> irest = 0,
>>> ntx = 1,
>>> cut = 9,
>>> ntb = 1,
>>> iwrap = 1,
>>> nmropt = 1,
>>> ntc = 2,
>>> ntf = 2,
>>> tempi = 0.0,
>>> temp0 = 300.0,
>>> ntt = 3,
>>> gamma_ln = 1.0,
>>> nstlim = 125000, dt = 0.002,
>>> ntpr = 100, ntwx = 500, ntwr = 1000,
>>> &end
>>> /
>>> &wt TYPE='END'
>>> DISANG=dist.RST
>> Can you post your dist.RST file?
>>> LISTOUT=dist.out
>>> /
>>> &end
>>>
>>> please guide me!
>>>
>>> thanks.
>>> Urszula
>>>
>>>
>>>
>>> -----------------------------------------
>>> Ta wiadomo?? zosta?a wys?ana z serwera Uniwersytetu Gda?skiego
>>> http://www.ug.edu.pl/
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> -----------------------------------------
> Ta wiadomo?? zosta?a wys?ana z serwera Uniwersytetu Gda?skiego
> http://www.ug.edu.pl/
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
-----------------------------------------
Ta wiadomo?? zosta?a wys?ana z serwera Uniwersytetu Gda?skiego
http://www.ug.edu.pl/
------------------------------
Message: 31
Date: Tue, 8 Apr 2014 09:49:49 -0400
From: Brian Radak <radak004.umn.edu>
Subject: Re: [AMBER] error in input file /nmropt=1
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAJrka9yyLA=Sq+b3dfu1qBScbWh9+DSS9LZY4qcdDtccWV7Mpg.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-2
DISANG and LISTOUT are not part of the &wt section, the go at the end of
the file. If there is a problem with dist.RST, it can probably be best
diagnosed by also using LISTIN=POUT.
Regards,
Brian
On Tue, Apr 8, 2014 at 9:03 AM, Asaminew Haile <ashaethio.gmail.com> wrote:
>
> On Apr 8, 2014, at 8:57 AM, Urszula Uciechowska <
> urszula.uciechowska.biotech.ug.edu.pl> wrote:
>
> > Dear AMBER users,
> > I'm trying to do some MD with sander.MPI and distance restraints
> (nmropt=1)
> > in AMBER 11.
> > No matter how I write the restraints I always get the same message:
> >
> > Flags:
> > getting new box info from bottom of inpcrd
> > | INFO: Old style inpcrd file read
> >
> > | peek_ewald_inpcrd: Box info found
> > |Largest sphere to fit in unit cell has radius = 42.653
> >
> >
> > My input file:
> > Heating
> > &cntrl
> > imin = 0,
> > irest = 0,
> > ntx = 1,
> > cut = 9,
> > ntb = 1,
> > iwrap = 1,
> > nmropt = 1,
> > ntc = 2,
> > ntf = 2,
> > tempi = 0.0,
> > temp0 = 300.0,
> > ntt = 3,
> > gamma_ln = 1.0,
> > nstlim = 125000, dt = 0.002,
> > ntpr = 100, ntwx = 500, ntwr = 1000,
> > &end
> > /
> > &wt TYPE='END'
> > DISANG=dist.RST
> Can you post your dist.RST file?
> > LISTOUT=dist.out
> > /
> > &end
> >
> > please guide me!
> >
> > thanks.
> > Urszula
> >
> >
> >
> > -----------------------------------------
> > Ta wiadomo?? zosta?a wys?ana z serwera Uniwersytetu Gda?skiego
> > http://www.ug.edu.pl/
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
------------------------------
Message: 32
Date: Tue, 8 Apr 2014 22:26:22 +0800
From: " jinfenghuang " <huangjinan00.qq.com>
Subject: [AMBER] Questions about the energy of H3O+
To: " amber-request " <amber-request.ambermd.org>
Cc: " amber " <amber.ambermd.org>
Message-ID: <tencent_7282E01D5E4473B77EB6157C.qq.com>
Content-Type: text/plain; charset="ISO-8859-1"
Dear Amber users, These days I try to use the MM_PBSA.py module to calculate the energy of the H2O and H3O+, but there exists a problem that puzzled me a lot. Firstly, I download the H3O+ parameters from the website
http://www.pharmacy.manchester.ac.uk/bryce/amber. According to the parameters ,I generate the H2O parameters which have the same frcmod file as the H3O+. But things goes strange, when I use the sander module of AMBER11 to calculate the gas energy of two molecule, the H3O+ has electrostatic energy while the H2O doesn't have.Results are as follows:
H2O
NSTEP ENERGY RMS GMAX NAME NUMBER
1 4.9643E-05 1.1479E-01 2.1413E-01 O 1
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
H3O+
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.9759E+02 3.8746E+01 7.0478E+01 Hw2 4
BOND = 0.0002 ANGLE = 0.0000 DIHED = 0.0000
VDWAALS = 0.0000 EEL = 197.5904 HBOND = 0.0000
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
Why the sander module recived the different gas energy of H3O+ and H2O which have the same frcmod file ? At the same tme, I'm sure that the three atoms of H3O+ are bonded to the oxgen.
------------------------------
Message: 33
Date: Tue, 8 Apr 2014 09:36:20 -0500
From: Milo Westler <milo.nmrfam.wisc.edu>
Subject: Re: [AMBER] REMD with pmemd.cuda
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CADRT24pQFhWHJbFK1eWZqa9EACGvAyvRMJaGq9jmGmz5tD7+Mw.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
So from the tutorial:
mpirun -np 8 $AMBERHOME/exe/sander.MPI -ng 8 -groupfile
equilibrate.groupfile
For multiple GPUs using pmemd.cuda.MPI, do I need to use the "setenv
CUDA_VISIBLE_DEVICES #" environmental variable?
or just
mpirun -np 8 $AMBERHOME/exe/pmemd.cuda.MPI -ng 8 -groupfile
equilibrate.groupfile
On Tue, Apr 8, 2014 at 6:45 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, 2014-04-08 at 03:37 -0400, Nhai wrote:
> > I dont think there is any difference.
>
> Except of course you need to use pmemd.cuda.MPI instead of sander.MPI as
> described in the relevant tutorial
> [http://ambermd.org/tutorials/advanced/tutorial7/] ;).
>
>
> >
> > Hai Nguyen
> >
> > > On Apr 7, 2014, at 9:04 PM, Milo Westler <milo.nmrfam.wisc.edu> wrote:
> > >
> > > Anyone know of a recent tutorial to do temperature REMD on multiple
> gpus?
> > >
> > > Thanks,
> > >
> > > --
> > > -- Milo
> > > ===================================================
> > > National Magnetic Resonance Facility at Madison
> > > An NIH-Supported Resource Center
> > >
> > > W. Milo Westler, Ph.D.
> > >
> > > NMRFAM Director
> > > Senior Scientist
> > > and
> > > Adjunct Professor
> > > Department of Biochemistry
> > > University of Wisconsin-Madison
> > > 433 Babcock Drive
> > > Madison, WI USA 53706-1544
> > > EMAIL: milo.nmrfam.wisc.edu
> > > PHONE: (608)-263-9599
> > > FAX: (608)-263-1722
> > > =======================================================================
> > > ========
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-- Milo
===================================================
National Magnetic Resonance Facility at Madison
An NIH-Supported Resource Center
W. Milo Westler, Ph.D.
NMRFAM Director
Senior Scientist
and
Adjunct Professor
Department of Biochemistry
University of Wisconsin-Madison
433 Babcock Drive
Madison, WI USA 53706-1544
EMAIL: milo.nmrfam.wisc.edu
PHONE: (608)-263-9599
FAX: (608)-263-1722
=======================================================================
========
------------------------------
Message: 34
Date: Tue, 8 Apr 2014 21:38:49 +0700
From: Setyanto Md <stwahyudi.md.gmail.com>
Subject: Re: [AMBER] Asking about using Vector Analysis: Thermo
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAM2h4exZba8dbDJDs7z2AYeEi-+nO5-Rk7giUcUk-36X40aLqQ.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear prof. Case, and Daniel Roe,
I am sorry if this email sent two times. I thought my email undelivered
since I got notification from postmaster (postmaster.gbaships.com) I don't
know why.
Thank's for the respond.
I just look into my outpur file thermo-2.dat and this is the contain of the
file :
======
*******************
- Thermochemistry -
*******************
temperature 298.150 kelvin
pressure 1.00000 atm
molecular mass (principal isotopes) 43349.19600 amu
principal moments of inertia (nuclei only) in amu-A**2:
10192003.92 11275397.53 12641992.89
rotational symmetry number 1
Warning-- assumption of classical behavior for rotation
may cause significant error
rotational temperatures (kelvin) 0.00000 0.00000 0.00000
zero point vibrational energy -1336561770.3 (joules/mol)
-319236.86933 (kcal/mol)
-509.0594837 (hartree/particle)
Warning-- 10249 vibrations have low frequencies and may represent hindered
internal rotations. The contributions printed below assume that
these
really are vibrations.
warning: setting vibrational entropy to zero for mode 13999 with vtemp =
-271964833.912749
warning: setting vibrational entropy to zero for mode 14000 with vtemp =
-206962223.144815
warning: setting vibrational entropy to zero for mode 14001 with vtemp =
-160303581.214612
warning: setting vibrational entropy to zero for mode 14002 with vtemp =
-93713731.426489
warning: setting vibrational entropy to zero for mode 14003 with vtemp =
-87684059.689750
warning: setting vibrational entropy to zero for mode 14004 with vtemp =
-79906661.448946
warning: setting vibrational entropy to zero for mode 14005 with vtemp =
-65836520.078644
warning: setting vibrational entropy to zero for mode 14006 with vtemp =
-63521944.525420
...
.
.
.
(there are almost 4000 line)
then continue with :
freq. E Cv S
cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin
--------------------------------------------------------------------------------
Total 37868394.472 -nan 17156.722
translational 0.888 2.979 57.778
rotational 0.888 2.979 59.973
vibrational 37868392.696 -nan 17038.971
1 0.101 0.592 1.986 17.124
2 0.233 0.592 1.986 15.472
3 0.313 0.592 1.986 14.883
4 0.520 0.592 1.986 13.875
5 0.619 0.592 1.986 13.530
6 0.788 0.592 1.986 13.051
7 1.498 0.592 1.986 11.774
8 1.907 0.592 1.986 11.294
9 2.232 0.592 1.986 10.982
10 2.634 0.592 1.986 10.654
11 3.154 0.592 1.986 10.296
12 3.218 0.592 1.986 10.256
.
.
.(until ..
.
.
9994 2696.302 3.855 0.001 0.000
9995 2702.649 3.864 0.001 0.000
9996 2707.884 3.871 0.001 0.000
9997 2725.954 3.897 0.001 0.000
9998 2733.508 3.908 0.001 0.000
9999 2739.742 3.917 0.001 0.000
=====
I have a question about this,.
======
freq. E Cv S
cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin
--------------------------------------------------------------------------------
Total 37868394.472 -nan 17156.722
translational 0.888 2.979 57.778
rotational 0.888 2.979 59.973
vibrational 37868392.696 -nan 17038.971
=======
The freq (cm**-1) is this a wave number ?
Then what is E (kcal/mol) ? is this the internal energy ?
the number 1 to 9999, I assume a number of my frame of of trajectory.
Why the Cv and Enthropy (S) was down to zero ?
Can we set the Temperature (298.15 K) and Pressure ? or it was extracted
from the trajectory ?
Dear Daniel Roe,
Yes it is "very" big output, I just select all atom of my protein include
with hydrogen, with total about 6000 atoms.
I'd like to know what is the my protein enthropy, Cv and Internal energy,
Should I calculate all atom or can I used Carbon Alpha only ?
Thanks for help.
I will re-calculate again since I did not make rms-fit. thanks to remind me.
On Thu, Apr 3, 2014 at 9:31 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Wed, Apr 2, 2014 at 9:10 PM, Setyanto Md <stwahyudi.md.gmail.com>
> wrote:
>
> >
> > Then after this execute I got file : mwthermo.dat as an output (size :
> 2.2
> > GB). It is a big output file.
> >
>
> That is a *very* big output file - how many atoms are you selecting? Be
> aware that you will need at least as many trajectory frames (and ideally
> more) as you have eigenvectors, otherwise 1 or more of your resulting
> eigenvalues will be zero, which may affect the quasiharmonic analysis in
> unexpected ways. Also, you should probably perform some sort of RMS-fit
> prior to calculation of the matrix to remove overall rotation/translation
> of your molecule (unless for some reason you want that reflected in the
> resulting matrix).
>
> -Dan
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
------------------------------
Message: 35
Date: Tue, 8 Apr 2014 08:46:33 -0600
From: Christina Bergonzo <cbergonzo.gmail.com>
Subject: Re: [AMBER] Really Weird Problem with Replica Exchange
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAMLwDJ3UJty9zVa=VjKVOGPW5dWCN-pApTqqCu5TDzZY89BTZw.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
The issue with the REMD may still be that you're not exchanging enough
times to see the acceptance % even out.
However, if you're trying to equilibrate the solvent environment, you can
run 10 or so copies of your system at the target or biological temperature
for several hundred nanoseconds (depends on types of ions present) with
different starting velocities and/or initial randomized ion positions to
sample the solvent environment.
-Christina
On Mon, Apr 7, 2014 at 2:21 PM, Christopher A Thiebaut
<cthieba.purdue.edu>wrote:
> Christina,
>
> The reason for the unuasually low high temperature is that I am actually
> trying to increase sampling of the water positions rather than the protein
> itself. Previously, we have compared the water positions around the active
> site derrived from MD simulations with those from the crystal structures
> and were not able to reproduce the experimental water positions. We think
> this may be because the crystal structures are taken at very low
> temperatures (But obviously a simple MD simulation of frozen water won't
> give us any change in water position). There are about 5,000 protein atoms
> and about 15,000 water molecules. I have SHAKEn the bonds to hydrogen
> within the protein to allow for a longer timestep dt=0.002.
>
> Christopher
>
> ----- Original Message -----
> From: "Christina Bergonzo" <cbergonzo.gmail.com>
> To: "AMBER Mailing List" <amber.ambermd.org>
> Sent: Monday, April 7, 2014 4:08:28 PM
> Subject: Re: [AMBER] Really Weird Problem with Replica Exchange
>
> Hi Christopher,
>
> Even if you have independently equilibrated the starting structures, it can
> take a while for the exchange probability to average out. This is system
> size dependent, and could take much longer than 30-ish exchanges. The
> exchange probability should start out at 0, though, and rise to whatever
> acceptance % you set up. The high initial acceptance tells me these
> replicas may be set up too closely, though I have used the same temperature
> generator before and gotten a good distribution out of it.
>
> In addition to what Carlos asked, how many atoms/how many water molecules
> are in your system? And what are you trying to sample here? A high
> temperature of ~300K seems too low to enhance sampling all that much. The
> T-REMD tutorial suggests using a range potentially up to 600K:
> http://ambermd.org/tutorials/advanced/tutorial7/
>
> -Christina
>
>
> On Mon, Apr 7, 2014 at 2:02 PM, Christopher A Thiebaut
> <cthieba.purdue.edu>wrote:
>
> > The initial structure was thermolysin with no ligand bound (will be doing
> > simulations with a variety of ligands bound later on) solvated in a TIP3P
> > truncated octahedron with periodic boundary conditions. I minimized the
> > solvent with the protein restrained, then minimized the system as a
> whole,
> > did a brief NVT simulation to get my system up to a reasonabe
> temperature,
> > which was in the middle of my range. Then I did a short NPT simulation
> (at
> > the same temperature, 1 atm pressure) to correct the density.
> Technically,
> > I know that density won't be quite right at most of my temperatures but I
> > don't have a huge temperature range so I don't think it should really be
> > troublingly off either. Then I did 32 separate equilibrations based on
> that
> > structure (at the replica exchange temperatures) before finally moving to
> > the replica exchange simulation.
> >
> > Christopher Thiebaut
> > Graduate Student
> > Purdue University
> > ----- Original Message -----
> > From: "Carlos Simmerling" <carlos.simmerling.gmail.com>
> > To: "AMBER Mailing List" <amber.ambermd.org>
> > Sent: Monday, April 7, 2014 3:48:18 PM
> > Subject: Re: [AMBER] Really Weird Problem with Replica Exchange
> >
> > what were the initial structures? were they pre-equilibrated that the
> right
> > Ts? tell us more about how you got to this point...
> >
> >
> > On Mon, Apr 7, 2014 at 2:58 PM, Christopher A Thiebaut
> > <cthieba.purdue.edu>wrote:
> >
> > > Helllo all,
> > >
> > > I am having what I imagine to be a very unusual problem running replica
> > > exchange of thermolysin solvated with explicit TIP3P water.
> > > The simulations will run without any error messages, but I am sure the
> > > results I am seeing are not meaningful because most replicas are
> > exchanging
> > > at most exchange attempts and even more so because the volocity scaling
> > is
> > > always 1.0 (meaning the volocites are not changed at all), except once
> > > during the first exchange. In addition, the total potential energy
> seems
> > > to be slowly increasing throughout the simulation which also should not
> > be
> > > happening.
> > >
> > > Here's a sample of my rem.log file so you can see what I'm talking
> about:
> > > # Rep#, Velocity Scaling, T, Eptot, Temp0, NewTemp0, Success rate
> > (i,i+1),
> > > ResStruct#
> > > # exchange 1
> > > 1 1.07 0.00-158275.28 270.00 310.44 0.00 -1
> > > 2 1.00 0.00-158841.35 271.23 272.47 2.00 -1
> > > 3 1.00 0.00-159708.30 272.47 271.23 0.00 -1
> > > 4 1.00 0.00-159547.14 273.71 274.96 2.00 -1
> > > 5 1.00 0.00-159457.82 274.96 273.71 0.00 -1
> > > 6 1.00 0.00-160730.25 276.21 277.46 2.00 -1
> > > 7 1.00 0.00-160858.37 277.46 276.21 0.00 -1
> > > 8 1.00 0.00-161155.52 278.73 279.98 2.00 -1
> > > 9 1.00 0.00-161044.87 279.98 278.73 0.00 -1
> > > 10 1.00 0.00-161039.89 281.25 282.53 2.00 -1
> > > 11 1.00 0.00-161096.24 282.53 281.25 0.00 -1
> > > 12 1.00 0.00-162494.74 283.81 285.09 2.00 -1
> > > 13 1.00 0.00-162767.85 285.09 283.81 0.00 -1
> > > 14 1.00 0.00-161902.49 286.38 287.68 2.00 -1
> > > 15 1.00 0.00-163145.99 287.68 286.38 0.00 -1
> > > 16 1.00 0.00-162901.03 288.97 290.28 2.00 -1
> > > 17 1.00 0.00-164106.69 290.28 288.97 0.00 -1
> > > 18 -1.00 0.00-163819.64 291.58 291.58 0.00 -1
> > > 19 -1.00 0.00-163549.67 292.90 292.90 0.00 -1
> > > 20 1.00 0.00-163950.79 294.21 295.53 2.00 -1
> > > 21 1.00 0.00-164690.76 295.53 294.21 0.00 -1
> > > 22 1.00 0.00-165187.80 296.86 298.19 2.00 -1
> > > 23 1.00 0.00-165377.17 298.19 296.86 0.00 -1
> > > 24 -1.00 0.00-164848.36 299.52 299.52 0.00 -1
> > > 25 -1.00 0.00-164797.83 300.86 300.86 0.00 -1
> > > 26 1.00 0.00-165237.92 302.21 303.56 2.00 -1
> > > 27 1.00 0.00-166216.65 303.56 302.21 0.00 -1
> > > 28 1.00 0.00-166127.19 304.91 306.27 2.00 -1
> > > 29 1.00 0.00-167327.09 306.27 304.91 0.00 -1
> > > 30 1.00 0.00-166545.00 307.64 309.01 2.00 -1
> > > 31 1.00 0.00-168071.75 309.01 307.64 0.00 -1
> > > 32 0.93 0.00-167178.34 310.44 270.00 2.00 -1
> > > ......................................................................
> > > # exchange 25
> > > 1 1.00 309.91-237311.34 309.01 307.64 0.08 -1
> > > 2 1.00 304.26-237005.16 302.21 303.56 1.04 -1
> > > 3 1.00 296.00-237356.49 296.86 298.19 1.04 -1
> > > 4 1.00 304.33-237213.57 304.91 306.27 0.96 -1
> > > 5 1.00 300.61-237074.41 299.52 300.86 0.96 -1
> > > 6 1.00 306.71-237010.94 307.64 309.01 0.88 -1
> > > 7 1.00 288.23-237533.96 286.38 287.68 1.04 -1
> > > 8 -1.00 309.85-237252.49 310.44 310.44 0.08 -1
> > > 9 1.00 289.99-237569.69 288.97 290.28 1.04 -1
> > > 10 1.00 307.03-237289.10 306.27 304.91 0.88 -1
> > > 11 1.00 296.78-237439.24 294.21 295.53 1.04 -1
> > > 12 1.00 302.80-237548.07 303.56 302.21 0.96 -1
> > > 13 1.00 291.19-237476.28 291.58 292.90 0.96 -1
> > > 14 1.00 298.13-237536.76 295.53 294.21 0.96 -1
> > > 15 1.00 284.22-237758.43 281.25 282.53 1.04 -1
> > > 16 1.00 291.28-237590.61 290.28 288.97 0.96 -1
> > > 17 1.00 277.07-237711.31 278.73 279.98 1.04 -1
> > > 18 1.00 277.52-237747.34 276.21 277.46 1.04 -1
> > > 19 1.00 300.95-237501.70 300.86 299.52 0.96 -1
> > > 20 1.00 297.03-237561.12 298.19 296.86 0.88 -1
> > > 21 1.00 282.63-237651.93 283.81 285.09 1.04 -1
> > > 22 -1.00 270.53-238135.36 270.00 270.00 0.56 -1
> > > 23 1.00 272.50-237928.60 271.23 272.47 0.88 -1
> > > 24 1.00 292.11-237641.94 292.90 291.58 0.96 -1
> > > 25 1.00 288.51-237686.39 287.68 286.38 0.96 -1
> > > 26 1.00 285.15-237838.02 285.09 283.81 0.96 -1
> > > 27 1.00 269.94-237998.93 272.47 271.23 0.72 -1
> > > 28 1.00 278.70-237910.14 279.98 278.73 0.96 -1
> > > 29 1.00 275.61-238021.61 274.96 273.71 0.96 -1
> > > 30 1.00 282.57-237916.92 282.53 281.25 0.96 -1
> > > 31 1.00 276.88-238031.26 277.46 276.21 0.96 -1
> > > 32 1.00 273.65-237788.60 273.71 274.96 0.96 -1
> > > # exchange 26
> > > 1 1.00 309.43-237528.66 307.64 306.27 0.85 -1
> > > 2 1.00 303.95-237551.08 303.56 304.91 1.00 -1
> > > 3 1.00 297.95-237809.91 298.19 299.52 0.92 -1
> > > 4 1.00 306.31-237657.13 306.27 307.64 0.92 -1
> > > 5 1.00 299.96-237577.66 300.86 302.21 1.00 -1
> > > 6 1.00 308.95-237472.73 309.01 310.44 0.15 -1
> > > 7 1.00 286.56-237844.08 287.68 288.97 1.00 -1
> > > 8 1.00 310.00-237519.31 310.44 309.01 0.08 -1
> > > 9 1.00 291.81-237729.64 290.28 291.58 1.00 -1
> > > 10 1.00 303.70-237715.75 304.91 303.56 0.92 -1
> > > 11 1.00 296.62-237700.83 295.53 296.86 1.00 -1
> > > 12 1.00 303.16-237772.77 302.21 300.86 1.00 -1
> > > 13 1.00 292.60-237770.36 292.90 294.21 1.00 -1
> > > 14 1.00 293.41-237816.24 294.21 292.90 1.00 -1
> > > 15 1.00 282.61-237999.04 282.53 283.81 1.00 -1
> > > 16 1.00 289.23-237958.84 288.97 287.68 1.00 -1
> > > 17 1.00 278.69-238016.41 279.98 281.25 1.00 -1
> > > 18 1.00 278.70-238051.34 277.46 278.73 1.00 -1
> > > 19 1.00 298.26-237923.06 299.52 298.19 0.92 -1
> > > 20 1.00 293.43-237819.98 296.86 295.53 1.00 -1
> > > 21 1.00 285.90-237872.36 285.09 286.38 1.00 -1
> > > 22 1.00 271.15-238192.37 270.00 271.23 0.62 -1
> > > 23 1.00 272.53-238207.17 272.47 273.71 0.77 -1
> > > 24 1.00 290.92-238028.52 291.58 290.28 0.92 -1
> > > 25 1.00 286.71-238159.73 286.38 285.09 1.00 -1
> > > 26 1.00 284.16-238189.10 283.81 282.53 1.00 -1
> > > 27 1.00 272.89-238264.83 271.23 270.00 0.85 -1
> > > 28 1.00 278.46-238289.12 278.73 277.46 1.00 -1
> > > 29 1.00 272.73-238268.68 273.71 272.47 0.92 -1
> > > 30 1.00 281.90-238206.67 281.25 279.98 1.00 -1
> > > 31 1.00 279.16-238218.60 276.21 274.96 1.00 -1
> > > 32 1.00 273.42-238084.44 274.96 276.21 1.00 -1
> > > # exchange 27
> > > 1 1.00 305.14-237896.37 306.27 304.91 0.89 -1
> > > 2 1.00 306.70-237688.11 304.91 306.27 0.96 -1
> > > 3 1.00 299.55-237906.46 299.52 300.86 0.96 -1
> > > 4 1.00 308.78-237779.85 307.64 309.01 0.89 -1
> > > 5 1.00 303.02-237740.95 302.21 303.56 1.04 -1
> > > 6 -1.00 312.04-237760.32 310.44 310.44 0.07 -1
> > > 7 1.00 289.44-238148.68 288.97 290.28 1.04 -1
> > > 8 1.00 308.40-237883.47 309.01 307.64 0.15 -1
> > > 9 1.00 293.62-238039.32 291.58 292.90 0.96 -1
> > > 10 1.00 303.22-237972.21 303.56 302.21 0.96 -1
> > > 11 1.00 298.26-238017.06 296.86 298.19 1.04 -1
> > > 12 1.00 302.52-238053.44 300.86 299.52 0.96 -1
> > > 13 1.00 297.91-238061.27 294.21 295.53 1.04 -1
> > > 14 1.00 293.39-238165.74 292.90 291.58 0.96 -1
> > > 15 1.00 286.69-238367.18 283.81 285.09 1.04 -1
> > > 16 1.00 285.33-238372.24 287.68 286.38 0.96 -1
> > > 17 1.00 280.09-238415.47 281.25 282.53 1.04 -1
> > > 18 1.00 279.14-238456.86 278.73 279.98 1.04 -1
> > > 19 1.00 297.69-238179.86 298.19 296.86 0.89 -1
> > > 20 1.00 293.78-238363.05 295.53 294.21 0.96 -1
> > > 21 1.00 286.04-238315.32 286.38 287.68 1.04 -1
> > > 22 1.00 269.92-238495.65 271.23 272.47 0.89 -1
> > > 23 1.00 272.51-238431.54 273.71 274.96 0.96 -1
> > > 24 1.00 289.51-238323.64 290.28 288.97 0.96 -1
> > > 25 1.00 285.80-238400.25 285.09 283.81 0.96 -1
> > > 26 1.00 284.11-238504.05 282.53 281.25 0.96 -1
> > > 27 -1.00 270.33-238639.41 270.00 270.00 0.59 -1
> > > 28 1.00 278.26-238633.26 277.46 276.21 0.96 -1
> > > 29 1.00 271.87-238758.14 272.47 271.23 0.74 -1
> > > 30 1.00 278.97-238406.37 279.98 278.73 0.96 -1
> > > 31 1.00 275.36-238642.13 274.96 273.71 0.96 -1
> > > 32 1.00 277.11-238336.79 276.21 277.46 1.04 -1
> > > # exchange 28
> > > 1 1.00 305.41-238178.28 304.91 303.56 0.93 -1
> > > 2 1.00 308.72-237888.75 306.27 307.64 0.93 -1
> > > 3 -1.00 299.85-238411.98 300.86 300.86 0.93 -1
> > > 4 1.00 308.47-237966.66 309.01 310.44 0.21 -1
> > > 5 1.00 302.86-237989.18 303.56 304.91 1.00 -1
> > > 6 1.00 310.64-238126.41 310.44 309.01 0.07 -1
> > > 7 1.00 291.09-238323.96 290.28 291.58 1.00 -1
> > > 8 1.00 306.54-238287.31 307.64 306.27 0.86 -1
> > > 9 1.00 292.28-238398.82 292.90 294.21 1.00 -1
> > > 10 -1.00 302.07-238374.29 302.21 302.21 1.00 -1
> > > 11 1.00 299.33-238367.94 298.19 299.52 0.93 -1
> > > 12 1.00 299.74-238329.33 299.52 298.19 0.93 -1
> > > 13 1.00 294.48-238329.94 295.53 296.86 1.00 -1
> > > 14 1.00 292.88-238512.89 291.58 290.28 0.93 -1
> > > 15 1.00 284.54-238592.77 285.09 286.38 1.00 -1
> > > 16 1.00 289.06-238586.60 286.38 285.09 1.00 -1
> > > 17 1.00 282.18-238604.33 282.53 283.81 1.00 -1
> > > 18 1.00 280.42-238498.62 279.98 281.25 1.00 -1
> > > 19 1.00 298.42-238339.10 296.86 295.53 1.00 -1
> > > 20 1.00 295.23-238501.82 294.21 292.90 1.00 -1
> > > 21 1.00 287.96-238622.69 287.68 288.97 1.00 -1
> > > 22 1.00 274.59-238791.23 272.47 273.71 0.79 -1
> > > 23 1.00 274.34-238732.39 274.96 276.21 1.00 -1
> > > 24 1.00 290.89-238503.91 288.97 287.68 1.00 -1
> > > 25 1.00 284.40-238719.97 283.81 282.53 1.00 -1
> > > 26 1.00 281.12-238697.12 281.25 279.98 1.00 -1
> > > 27 1.00 271.44-238981.93 270.00 271.23 0.64 -1
> > > 28 1.00 277.56-238877.61 276.21 274.96 1.00 -1
> > > 29 1.00 272.58-239072.51 271.23 270.00 0.86 -1
> > > 30 1.00 279.19-238902.86 278.73 277.46 1.00 -1
> > > 31 1.00 274.58-238952.80 273.71 272.47 0.93 -1
> > > 32 1.00 278.29-238672.97 277.46 278.73 1.00 -1
> > > # exchange 29
> > > 1 1.00 303.10-238482.53 303.56 302.21 0.97 -1
> > > 2 1.00 308.47-238268.33 307.64 309.01 0.90 -1
> > > 3 1.00 300.90-238576.50 300.86 299.52 0.90 -1
> > > 4 -1.00 310.92-238315.71 310.44 310.44 0.07 -1
> > > 5 1.00 304.45-238317.36 304.91 306.27 0.97 -1
> > > 6 1.00 307.80-238499.68 309.01 307.64 0.21 -1
> > > 7 1.00 291.95-238596.78 291.58 292.90 0.97 -1
> > > 8 1.00 306.74-238454.39 306.27 304.91 0.90 -1
> > > 9 1.00 294.77-238569.62 294.21 295.53 1.03 -1
> > > 10 1.00 303.24-238531.15 302.21 303.56 1.03 -1
> > > 11 1.00 299.01-238638.43 299.52 300.86 0.97 -1
> > > 12 1.00 299.36-238835.63 298.19 296.86 0.90 -1
> > > 13 1.00 298.09-238588.55 296.86 298.19 1.03 -1
> > > 14 1.00 291.63-238777.70 290.28 288.97 0.97 -1
> > > 15 1.00 286.85-239032.37 286.38 287.68 1.03 -1
> > > 16 1.00 285.69-238846.49 285.09 283.81 0.97 -1
> > > 17 1.00 282.94-238892.18 283.81 285.09 1.03 -1
> > > 18 1.00 281.44-238894.57 281.25 282.53 1.03 -1
> > > 19 1.00 296.81-238719.29 295.53 294.21 0.97 -1
> > > 20 1.00 293.05-238860.89 292.90 291.58 0.97 -1
> > > 21 1.00 286.63-238769.89 288.97 290.28 1.03 -1
> > > 22 1.00 276.10-238983.43 273.71 274.96 0.97 -1
> > > 23 1.00 278.03-238930.08 276.21 277.46 1.03 -1
> > > 24 1.00 286.91-238958.25 287.68 286.38 0.97 -1
> > > 25 1.00 282.26-239046.26 282.53 281.25 0.97 -1
> > > 26 1.00 279.78-239123.91 279.98 278.73 0.97 -1
> > > 27 1.00 273.78-239151.24 271.23 272.47 0.90 -1
> > > 28 1.00 275.98-239171.49 274.96 273.71 0.97 -1
> > > 29 -1.00 269.99-239317.35 270.00 270.00 0.62 -1
> > > 30 1.00 276.91-239191.40 277.46 276.21 0.97 -1
> > > 31 1.00 272.73-239255.54 272.47 271.23 0.76 -1
> > > 32 1.00 279.96-238888.03 278.73 279.98 1.03 -1
> > > # exchange 30
> > > 1 1.00 302.64-238842.01 302.21 300.86 1.00 -1
> > > 2 1.00 308.63-238427.17 309.01 310.44 0.27 -1
> > > 3 1.00 299.84-238911.95 299.52 298.19 0.93 -1
> > > 4 1.00 309.86-238515.73 310.44 309.01 0.07 -1
> > > 5 1.00 307.42-238560.64 306.27 307.64 0.93 -1
> > > 6 1.00 307.48-238702.43 307.64 306.27 0.87 -1
> > > 7 1.00 292.53-238839.87 292.90 294.21 1.00 -1
> > > 8 1.00 306.00-238777.41 304.91 303.56 0.93 -1
> > > 9 1.00 297.32-238947.72 295.53 296.86 1.00 -1
> > > 10 1.00 304.05-238883.82 303.56 304.91 1.00 -1
> > > 11 1.00 302.57-238780.54 300.86 302.21 0.93 -1
> > > 12 1.00 292.21-238910.66 296.86 295.53 1.00 -1
> > > 13 1.00 298.97-238780.23 298.19 299.52 0.93 -1
> > > 14 1.00 286.86-239171.01 288.97 287.68 1.00 -1
> > > 15 1.00 290.28-239150.80 287.68 288.97 1.00 -1
> > > 16 1.00 282.76-239323.47 283.81 282.53 1.00 -1
> > > 17 1.00 284.27-239063.46 285.09 286.38 1.00 -1
> > > 18 1.00 281.82-239049.67 282.53 283.81 1.00 -1
> > > 19 1.00 292.78-239024.98 294.21 292.90 1.00 -1
> > > 20 1.00 293.24-239149.18 291.58 290.28 0.93 -1
> > > 21 1.00 291.56-239013.66 290.28 291.58 1.00 -1
> > > 22 1.00 276.39-239397.26 274.96 276.21 1.00 -1
> > > 23 1.00 278.04-239172.39 277.46 278.73 1.00 -1
> > > 24 1.00 287.81-239189.88 286.38 285.09 1.00 -1
> > > 25 1.00 281.80-239499.51 281.25 279.98 1.00 -1
> > > 26 1.00 279.53-239167.74 278.73 277.46 1.00 -1
> > > 27 1.00 272.13-239418.19 272.47 273.71 0.80 -1
> > > 28 1.00 273.73-239459.18 273.71 272.47 0.93 -1
> > > 29 1.00 269.25-239534.80 270.00 271.23 0.67 -1
> > > 30 1.00 278.19-239456.51 276.21 274.96 1.00 -1
> > > 31 1.00 267.89-239471.35 271.23 270.00 0.87 -1
> > > 32 1.00 282.43-239161.13 279.98 281.25 1.00 -1
> > > # exchange 31
> > > 1 1.00 301.00-238974.09 300.86 299.52 0.90 -1
> > > 2 -1.00 309.61-238660.96 310.44 310.44 0.06 -1
> > > 3 1.00 299.18-239060.07 298.19 296.86 0.90 -1
> > > 4 1.00 310.05-238867.09 309.01 307.64 0.26 -1
> > > 5 1.00 305.97-238751.83 307.64 309.01 0.90 -1
> > > 6 1.00 303.80-238862.17 306.27 304.91 0.90 -1
> > > 7 1.00 294.92-239133.23 294.21 295.53 1.03 -1
> > > 8 1.00 300.79-239134.89 303.56 302.21 0.97 -1
> > > 9 1.00 295.27-239078.59 296.86 298.19 1.03 -1
> > > 10 1.00 307.38-238976.05 304.91 306.27 0.97 -1
> > > 11 1.00 299.93-239007.75 302.21 303.56 1.03 -1
> > > 12 1.00 296.23-239266.13 295.53 294.21 0.97 -1
> > > 13 1.00 300.31-238964.11 299.52 300.86 0.97 -1
> > > 14 1.00 288.87-239491.68 287.68 286.38 0.97 -1
> > > 15 1.00 288.87-239181.78 288.97 290.28 1.03 -1
> > > 16 1.00 283.85-239447.44 282.53 281.25 0.97 -1
> > > 17 1.00 286.93-239387.00 286.38 287.68 1.03 -1
> > > 18 1.00 285.28-239293.13 283.81 285.09 1.03 -1
> > > 19 1.00 294.38-239262.60 292.90 291.58 0.97 -1
> > > 20 1.00 291.41-239473.95 290.28 288.97 0.97 -1
> > > 21 1.00 291.99-239025.10 291.58 292.90 0.97 -1
> > > 22 1.00 277.99-239464.65 276.21 277.46 1.03 -1
> > > 23 1.00 280.21-239389.24 278.73 279.98 1.03 -1
> > > 24 1.00 285.12-239418.39 285.09 283.81 0.97 -1
> > > 25 1.00 279.17-239630.47 279.98 278.73 0.97 -1
> > > 26 1.00 276.92-239490.22 277.46 276.21 0.97 -1
> > > 27 -1.00 273.11-239656.31 273.71 273.71 0.90 -1
> > > 28 1.00 272.29-239793.97 272.47 271.23 0.77 -1
> > > 29 1.00 271.67-239750.30 271.23 272.47 0.90 -1
> > > 30 -1.00 273.12-239533.78 274.96 274.96 0.97 -1
> > > 31 -1.00 268.90-239618.69 270.00 270.00 0.65 -1
> > > 32 1.00 281.96-239330.79 281.25 282.53 1.03 -1
> > > # exchange 32
> > > 1 1.00 299.58-239343.43 299.52 298.19 0.94 -1
> > > 2 1.00 311.50-238980.95 310.44 309.01 0.06 -1
> > > 3 1.00 295.85-239184.29 296.86 295.53 1.00 -1
> > > 4 -1.00 308.17-239136.45 307.64 307.64 0.88 -1
> > > 5 1.00 308.06-238988.58 309.01 310.44 0.31 -1
> > > 6 1.00 305.13-239138.99 304.91 303.56 0.94 -1
> > > 7 1.00 297.85-239308.56 295.53 296.86 1.00 -1
> > > 8 1.00 301.01-239380.21 302.21 300.86 1.00 -1
> > > 9 1.00 298.53-239203.29 298.19 299.52 0.94 -1
> > > 10 -1.00 304.70-239232.45 306.27 306.27 0.88 -1
> > > 11 1.00 302.69-239202.78 303.56 304.91 1.00 -1
> > > 12 1.00 294.94-239499.66 294.21 292.90 1.00 -1
> > > 13 1.00 300.69-239395.23 300.86 302.21 0.94 -1
> > > 14 1.00 286.37-239695.11 286.38 285.09 1.00 -1
> > > 15 1.00 291.36-239520.08 290.28 291.58 1.00 -1
> > > 16 1.00 281.85-239685.86 281.25 279.98 1.00 -1
> > > 17 1.00 286.91-239521.64 287.68 288.97 1.00 -1
> > > 18 1.00 285.86-239469.74 285.09 286.38 1.00 -1
> > > 19 1.00 291.53-239557.96 291.58 290.28 0.94 -1
> > > 20 1.00 287.61-239612.47 288.97 287.68 1.00 -1
> > > 21 1.00 295.50-239511.96 292.90 294.21 1.00 -1
> > > 22 1.00 277.08-239728.20 277.46 278.73 1.00 -1
> > > 23 1.00 281.02-239549.47 279.98 281.25 1.00 -1
> > > 24 1.00 285.24-239811.81 283.81 282.53 1.00 -1
> > > 25 1.00 280.54-239919.66 278.73 277.46 1.00 -1
> > > 26 1.00 275.03-239906.59 276.21 274.96 1.00 -1
> > > 27 -1.00 273.96-239787.93 273.71 273.71 0.88 -1
> > > 28 1.00 271.41-239907.75 271.23 270.00 0.88 -1
> > > 29 -1.00 272.49-239881.87 272.47 272.47 0.75 -1
> > > 30 1.00 273.86-239793.13 274.96 276.21 1.00 -1
> > > 31 1.00 270.74-239929.02 270.00 271.23 0.69 -1
> > > 32 1.00 284.17-239559.23 282.53 283.81 1.00 -1
> > > # exchange 33
> > > 1 1.00 298.56-239647.71 298.19 296.86 0.91 -1
> > > 2 1.00 310.32-239222.61 309.01 307.64 0.30 -1
> > > 3 1.00 294.15-239565.38 295.53 294.21 0.97 -1
> > > 4 1.00 303.38-239211.71 307.64 309.01 0.91 -1
> > > 5 -1.00 311.39-239214.75 310.44 310.44 0.06 -1
> > > 6 1.00 303.15-239587.23 303.56 302.21 0.97 -1
> > > 7 1.00 295.82-239452.66 296.86 298.19 1.03 -1
> > > 8 1.00 301.75-239706.01 300.86 299.52 0.91 -1
> > > 9 1.00 299.23-239590.40 299.52 300.86 0.97 -1
> > > 10 1.00 306.48-239596.64 306.27 304.91 0.85 -1
> > > 11 1.00 304.11-239317.37 304.91 306.27 0.97 -1
> > > 12 1.00 295.12-239733.48 292.90 291.58 0.97 -1
> > > 13 1.00 302.37-239381.64 302.21 303.56 1.03 -1
> > > 14 1.00 285.43-239993.86 285.09 283.81 0.97 -1
> > > 15 1.00 293.03-239827.37 291.58 292.90 0.97 -1
> > > 16 1.00 281.71-240076.80 279.98 278.73 0.97 -1
> > > 17 1.00 287.46-239707.00 288.97 290.28 1.03 -1
> > > 18 1.00 287.92-239662.53 286.38 287.68 1.03 -1
> > > 19 1.00 289.38-239765.38 290.28 288.97 0.97 -1
> > > 20 1.00 287.47-239790.23 287.68 286.38 0.97 -1
> > > 21 1.00 293.81-239572.60 294.21 295.53 1.03 -1
> > > 22 1.00 279.07-239939.90 278.73 279.98 1.03 -1
> > > 23 1.00 279.45-239795.77 281.25 282.53 1.03 -1
> > > 24 1.00 282.05-240026.98 282.53 281.25 0.97 -1
> > > 25 1.00 280.62-240229.59 277.46 276.21 0.97 -1
> > > 26 1.00 276.37-240004.49 274.96 273.71 0.97 -1
> > > 27 1.00 274.39-240117.97 273.71 274.96 0.91 -1
> > > 28 -1.00 271.27-240176.99 270.00 270.00 0.67 -1
> > > 29 1.00 272.88-240227.77 272.47 271.23 0.73 -1
> > > 30 1.00 277.02-240107.91 276.21 277.46 1.03 -1
> > > 31 1.00 271.63-240007.57 271.23 272.47 0.91 -1
> > > 32 1.00 283.63-239721.84 283.81 285.09 1.03 -1
> > >
> > > Temperatures were selected using: http://folding.bmc.uu.se/remd/
> > > The temperatures are:
> > > 270.00, 271.24, 272.48, 273.73, 274.98, 276.24, 277.50, 278.76, 280.04,
> > > 281.31, 282.59, 283.87, 285.17, 286.46, 287.76, 289.06, 290.37, 291.68,
> > > 293.00, 294.32, 295.65, 296.98, 298.32, 299.66, 301.01, 302.35, 303.71,
> > > 305.07, 306.43, 307.81, 309.18, 310.57
> > >
> > > These temperatures are based on 102229 degrees of freedom for the
> system
> > > and a desired exchange probability of .22. According to my mdout
> files,
> > > the system actually has 101423 degrees of freedom. So I think the
> > > temperatures may be a bit off, but I would be very surprised if they
> were
> > > responsible for anything as drastically weird as what I'm seeing.
> > >
> > > Has anybody seen these types of results before? What was the the
> cause?
> > > How did yo solve it?
> > >
> > > Christopher Thiebaut
> > > Graduate Student
> > > Purdue University
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
>
> ---------------------------------------------------------------------------------------
> Christina Bergonzo, PhD
> Postdoctoral Researcher
> Department of Medicinal Chemistry, University of Utah
> 30 South 2000 East, Rm. 201
> Salt Lake City, UT 84112-5820
> Office: L.S. Skaggs Pharmacy Research Institute, Rm.4290
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652 / Fax: (801) 585-6208
>
> ---------------------------------------------------------------------------------------
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------------------------------------------------------
Christina Bergonzo, PhD
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
30 South 2000 East, Rm. 201
Salt Lake City, UT 84112-5820
Office: L.S. Skaggs Pharmacy Research Institute, Rm.4290
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652 / Fax: (801) 585-6208
---------------------------------------------------------------------------------------
------------------------------
Message: 36
Date: Tue, 8 Apr 2014 09:46:45 -0500
From: Milo Westler <milo.nmrfam.wisc.edu>
Subject: Re: [AMBER] REMD with pmemd.cuda
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CADRT24o2mhto3-3XSq1341VQcNXuyryZLh6uWQ+_L3ATrxgoZQ.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Sorry, that should have been (for REMD instead of equilibrate):
mpirun -np 8 $AMBERHOME/exe/pmemd.cuda.MPI -ng 8 -groupfile remd.groupfile
On Tue, Apr 8, 2014 at 9:36 AM, Milo Westler <milo.nmrfam.wisc.edu> wrote:
>
> So from the tutorial:
>
> mpirun -np 8 $AMBERHOME/exe/sander.MPI -ng 8 -groupfile
> equilibrate.groupfile
>
> For multiple GPUs using pmemd.cuda.MPI, do I need to use the "setenv
> CUDA_VISIBLE_DEVICES #" environmental variable?
>
> or just
>
> mpirun -np 8 $AMBERHOME/exe/pmemd.cuda.MPI -ng 8 -groupfile
> equilibrate.groupfile
>
>
>
>
> On Tue, Apr 8, 2014 at 6:45 AM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> On Tue, 2014-04-08 at 03:37 -0400, Nhai wrote:
>> > I dont think there is any difference.
>>
>> Except of course you need to use pmemd.cuda.MPI instead of sander.MPI as
>> described in the relevant tutorial
>> [http://ambermd.org/tutorials/advanced/tutorial7/] ;).
>>
>>
>> >
>> > Hai Nguyen
>> >
>> > > On Apr 7, 2014, at 9:04 PM, Milo Westler <milo.nmrfam.wisc.edu>
>> wrote:
>> > >
>> > > Anyone know of a recent tutorial to do temperature REMD on multiple
>> gpus?
>> > >
>> > > Thanks,
>> > >
>> > > --
>> > > -- Milo
>> > > ===================================================
>> > > National Magnetic Resonance Facility at Madison
>> > > An NIH-Supported Resource Center
>> > >
>> > > W. Milo Westler, Ph.D.
>> > >
>> > > NMRFAM Director
>> > > Senior Scientist
>> > > and
>> > > Adjunct Professor
>> > > Department of Biochemistry
>> > > University of Wisconsin-Madison
>> > > 433 Babcock Drive
>> > > Madison, WI USA 53706-1544
>> > > EMAIL: milo.nmrfam.wisc.edu
>> > > PHONE: (608)-263-9599
>> > > FAX: (608)-263-1722
>> > >
>> =======================================================================
>> > > ========
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> -- Milo
> ===================================================
> National Magnetic Resonance Facility at Madison
> An NIH-Supported Resource Center
>
> W. Milo Westler, Ph.D.
>
> NMRFAM Director
> Senior Scientist
> and
> Adjunct Professor
> Department of Biochemistry
> University of Wisconsin-Madison
> 433 Babcock Drive
> Madison, WI USA 53706-1544
> EMAIL: milo.nmrfam.wisc.edu
> PHONE: (608)-263-9599
> FAX: (608)-263-1722
> =======================================================================
> ========
>
--
-- Milo
===================================================
National Magnetic Resonance Facility at Madison
An NIH-Supported Resource Center
W. Milo Westler, Ph.D.
NMRFAM Director
Senior Scientist
and
Adjunct Professor
Department of Biochemistry
University of Wisconsin-Madison
433 Babcock Drive
Madison, WI USA 53706-1544
EMAIL: milo.nmrfam.wisc.edu
PHONE: (608)-263-9599
FAX: (608)-263-1722
=======================================================================
========
------------------------------
Message: 37
Date: Tue, 08 Apr 2014 10:59:20 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] REMD with pmemd.cuda
To: amber.ambermd.org
Message-ID: <1396969160.19418.8.camel.heroes-out.rutgers.edu>
Content-Type: text/plain; charset="UTF-8"
On Tue, 2014-04-08 at 09:36 -0500, Milo Westler wrote:
> So from the tutorial:
>
> mpirun -np 8 $AMBERHOME/exe/sander.MPI -ng 8 -groupfile
> equilibrate.groupfile
>
> For multiple GPUs using pmemd.cuda.MPI, do I need to use the "setenv
> CUDA_VISIBLE_DEVICES #" environmental variable?
My suggestion is to just make sure that you are using every GPU on every
node you are assigned to avoid the CUDA_VISIBLE_DEVICES problem
altogether. It's not entirely straightforward to make sure that
CUDA_VISIBLE_DEVICES is propagated to all of the threads correctly.
The UF HPC staff has written a nifty little wrapper that will handle
this 'correctly' using the GPU-aware torque scheduler:
http://wiki.hpc.ufl.edu/doc/CUDA_PBS
Of course this really only works if _everyone_ uses the cluster
'correctly' (i.e., only uses GPUs they're assigned to by the scheduler).
If you are given exclusive access to each node's GPU resources,
CUDA_VISIBLE_DEVICES becomes unnecessary.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
Message: 38
Date: Tue, 8 Apr 2014 10:57:40 -0400
From: Lara rajam <lara.4884.gmail.com>
Subject: Re: [AMBER] antechamber
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAPQ+66BYQZFq8x_=mf88RRpTihqJixaGcyntMEGWxSYvkz5zHg.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear Amber
Thank you , that tutorial is working good
I am able to generate the parameter files .
On Mon, Apr 7, 2014 at 6:00 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Apr 7, 2014 at 4:24 PM, Lara rajam <lara.4884.gmail.com> wrote:
>
> > I can understand the gaff parameters are in lower case , thanks you for
> > your suggestion
> > but still i am not able to build the parameter it says the error as below
> >
>
> You didn't say what you actually did. Did you source leaprc.gaff? Did
> you run parmchk to generate an frcmod file from the mol2 in order to fill
> in missing parameters? Have you run this tutorial successfully:
> http://ambermd.org/tutorials/basic/tutorial4b/ ?
>
>
>
> >
> > Building topology.
> > Building atom parameters.
> > Building bond parameters.
> > Building angle parameters.
> > Could not find angle parameter: s6 - os - ca
> > Could not find angle parameter: c - ca - os
> > Could not find angle parameter: c - ca - cc
> > Could not find angle parameter: ca - os - s6
> > Could not find angle parameter: ca - cc - ca
> > Could not find angle parameter: os - ca - cc
> > Could not find angle parameter: ca - os - s6
> > Could not find angle parameter: ca - os - s6
> > Building proper torsion parameters.
> > ** No torsion terms for ca-os-cc-ca
> > ** No torsion terms for ca-os-cc-ca
> > ** No torsion terms for os-cc-ca-c
> > ** No torsion terms for os-cc-ca-os
> > ** No torsion terms for os-cc-ca-ca
> > ** No torsion terms for os-cc-ca-ca
> > ** No torsion terms for c-ca-cc-ca
> > ** No torsion terms for ca-cc-ca-ca
> > ** No torsion terms for ca-cc-ca-ca
> > ** No torsion terms for os-ca-cc-ca
> > Building improper torsion parameters.
> > total 6 improper torsions applied
> >
> > How to fix these improper terms
> >
>
> These are missing angles and dihedrals, NOT missing improper torsions.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
------------------------------
Message: 39
Date: Tue, 08 Apr 2014 11:52:12 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] Questions about the energy of H3O+
To: amber.ambermd.org
Message-ID: <1396972332.19418.13.camel.heroes-out.rutgers.edu>
Content-Type: text/plain; charset="UTF-8"
On Tue, 2014-04-08 at 22:26 +0800, jinfenghuang wrote:
> Dear Amber users, These days I try to use the MM_PBSA.py module to
> calculate the energy of the H2O and H3O+, but there exists a problem
> that puzzled me a lot. Firstly, I download the H3O+ parameters from
> the website http://www.pharmacy.manchester.ac.uk/bryce/amber.
> According to the parameters ,I generate the H2O parameters which have
> the same frcmod file as the H3O+. But things goes strange, when I use
> the sander module of AMBER11 to calculate the gas energy of two
> molecule, the H3O+ has electrostatic energy while the H2O doesn't
> have.Results are as follows:
> H2O
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 4.9643E-05 1.1479E-01 2.1413E-01 O 1
>
>
> BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
> VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
>
>
> H3O+
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 1.9759E+02 3.8746E+01 7.0478E+01 Hw2 4
>
>
> BOND = 0.0002 ANGLE = 0.0000 DIHED = 0.0000
> VDWAALS = 0.0000 EEL = 197.5904 HBOND = 0.0000
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
>
>
> Why the sander module recived the different gas energy of H3O+ and H2O
> which have the same frcmod file ?
They are different molecules! Consider an alanine tripeptide and an
alanine dipeptide modeled by the same force field. You certainly would
not expect their gas phase energies to be the same since they are
different systems and form different interactions.
> At the same tme, I'm sure that the three atoms of H3O+ are bonded to
> the oxgen.
If all you have is a single H3O+ molecule in which the oxygen is bound
to all 3 hydrogens, it's impossible to have a EEL value that is
non-zero. The reason is that nonbonded interactions between atoms that
are separated by 1 or 2 bonds (that form bonds or angles) is omitted
from the calculation. In H3O+, all atoms are separated by 2 bonds or
fewer, which means that no nonbonded interactions are computed.
Therefore, at least one of the hydrogens must not have a physical bond
to the oxygen. You can use the "printBonds" command in ParmEd to get a
full listing of the bonds that are present in the topology file.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
Message: 40
Date: Tue, 8 Apr 2014 12:02:30 -0400
From: David A Case <case.biomaps.rutgers.edu>
Subject: Re: [AMBER] error in input file /nmropt=1
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20140408160230.GA66733.biomaps.rutgers.edu>
Content-Type: text/plain; charset=us-ascii
On Tue, Apr 08, 2014, Urszula Uciechowska wrote:
>
> Flags:
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
>
> | peek_ewald_inpcrd: Box info found
> |Largest sphere to fit in unit cell has radius = 42.653
This is OK. Something bad happened later. Usual advice: set ntpr=1 and
nstlim=20. See if you get more information that will help resolve the
problem.
...dac
------------------------------
Message: 41
Date: Tue, 8 Apr 2014 12:08:44 -0400
From: David A Case <case.biomaps.rutgers.edu>
Subject: Re: [AMBER] Asking about using Vector Analysis: Thermo
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20140408160844.GB66733.biomaps.rutgers.edu>
Content-Type: text/plain; charset=us-ascii
On Tue, Apr 08, 2014, Setyanto Md wrote:
> Warning-- 10249 vibrations have low frequencies and may represent hindered
> internal rotations. The contributions printed below assume that
> these
> really are vibrations.
> warning: setting vibrational entropy to zero for mode 13999 with vtemp =
> -271964833.912749
I'm guessing(?) that you did a quasiharmonic analysis, but have fewer
snapshots than you have degrees of freedom (i.e. than 3*natom).
If so, you need to correct this, e.g. by having more snapshots, or by
requesting fewer vibrational frequencies.
For the future, it would be good for the code to trap this sort of error,
but for now, you have to take care yourself.
Of course, if my guess is wrong, then something else is going on.
...dac
------------------------------
Message: 42
Date: Tue, 8 Apr 2014 11:49:08 -0500
From: Milo Westler <milo.nmrfam.wisc.edu>
Subject: Re: [AMBER] REMD with pmemd.cuda
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
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Fortunately, the GPUs are all mine.
Thanks for the wrapper, I'll give it a try.
On Tue, Apr 8, 2014 at 9:59 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, 2014-04-08 at 09:36 -0500, Milo Westler wrote:
> > So from the tutorial:
> >
> > mpirun -np 8 $AMBERHOME/exe/sander.MPI -ng 8 -groupfile
> > equilibrate.groupfile
> >
> > For multiple GPUs using pmemd.cuda.MPI, do I need to use the "setenv
> > CUDA_VISIBLE_DEVICES #" environmental variable?
>
> My suggestion is to just make sure that you are using every GPU on every
> node you are assigned to avoid the CUDA_VISIBLE_DEVICES problem
> altogether. It's not entirely straightforward to make sure that
> CUDA_VISIBLE_DEVICES is propagated to all of the threads correctly.
>
> The UF HPC staff has written a nifty little wrapper that will handle
> this 'correctly' using the GPU-aware torque scheduler:
>
> http://wiki.hpc.ufl.edu/doc/CUDA_PBS
>
> Of course this really only works if _everyone_ uses the cluster
> 'correctly' (i.e., only uses GPUs they're assigned to by the scheduler).
> If you are given exclusive access to each node's GPU resources,
> CUDA_VISIBLE_DEVICES becomes unnecessary.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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--
-- Milo
===================================================
National Magnetic Resonance Facility at Madison
An NIH-Supported Resource Center
W. Milo Westler, Ph.D.
NMRFAM Director
Senior Scientist
and
Adjunct Professor
Department of Biochemistry
University of Wisconsin-Madison
433 Babcock Drive
Madison, WI USA 53706-1544
EMAIL: milo.nmrfam.wisc.edu
PHONE: (608)-263-9599
FAX: (608)-263-1722
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Received on Thu Apr 10 2014 - 19:30:02 PDT
