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
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
---------------------------------------------------------------------------------------
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
---------------------------------------------------------------------------------------
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Received on Mon Apr 07 2014 - 13:30:04 PDT
