The problem is that I'm not only trying to sample the biological temperature ensemble. I am also interested in seeing the low temperature ensemble, which I cannot really do as you suggest at the low temperature, as the water should be frozen near their starting positions.
After many more rounds of replica exchange, the exchange fequency are still unreasonably high, but have come down a little:
# exchange 79
1 1.00 275.38-244831.05 273.71 274.96 0.81 -1
2 1.00 279.49-244990.76 279.98 278.73 0.89 -1
3 1.00 298.89-244526.61 298.19 296.86 0.91 -1
4 -1.00 295.95-244496.19 295.53 295.53 0.89 -1
5 1.00 291.07-244569.56 290.28 288.97 0.91 -1
6 1.00 270.99-244907.44 271.23 272.47 0.76 -1
7 1.00 298.69-244423.45 300.86 299.52 0.89 -1
8 1.00 274.76-244919.34 274.96 273.71 0.71 -1
9 1.00 305.26-244475.61 303.56 302.21 0.89 -1
10 1.00 273.72-244958.58 276.21 277.46 0.81 -1
11 1.00 276.11-244932.81 277.46 276.21 0.84 -1
12 1.00 303.57-244468.98 302.21 303.56 0.94 -1
13 1.00 296.16-244515.94 296.86 298.19 0.94 -1
14 1.00 303.38-244392.55 304.91 306.27 0.91 -1
15 1.00 278.82-244884.81 278.73 279.98 0.84 -1
16 1.00 291.47-244567.89 291.58 292.90 0.86 -1
17 1.00 306.35-244337.11 306.27 304.91 0.81 -1
18 1.00 282.77-244827.21 282.53 281.25 0.89 -1
19 1.00 284.39-244725.67 286.38 287.68 0.84 -1
20 1.00 274.02-244991.41 272.47 271.23 0.81 -1
21 1.00 288.43-244555.60 288.97 290.28 0.89 -1
22 -1.00 312.95-244137.51 310.44 310.44 0.03 -1
23 1.00 292.55-244691.55 292.90 291.58 0.91 -1
24 1.00 283.04-244674.30 283.81 285.09 0.89 -1
25 -1.00 270.18-244984.45 270.00 270.00 0.58 -1
26 1.00 306.76-244249.03 307.64 309.01 0.84 -1
27 1.00 284.72-244649.97 285.09 283.81 0.84 -1
28 1.00 297.21-244399.98 299.52 300.86 0.86 -1
29 -1.00 295.90-244605.15 294.21 294.21 0.86 -1
30 1.00 281.88-244843.69 281.25 282.53 0.89 -1
31 1.00 309.55-244288.13 309.01 307.64 0.56 -1
32 1.00 286.96-244678.21 287.68 286.38 0.91 -1
Something that seems really pathological to me is that the velocity scaling keeps coming out to 1.00 every exchange. Shouldn't it pretty much never come out to exacltly 1.00? This seems to imply that the velocities should be the same for all of those temperatures accross the entire distribution, which is obviously not true. Has anyone very had the velocity scaling keep coming out at 1.00? What does that mean?
Chris Thiebaut
----- Original Message -----
From: "Christina Bergonzo" <cbergonzo.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Tuesday, April 8, 2014 10:46:33 AM
Subject: Re: [AMBER] Really Weird Problem with Replica Exchange
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
>
> ---------------------------------------------------------------------------------------
> _______________________________________________
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>
> _______________________________________________
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> 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
---------------------------------------------------------------------------------------
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Received on Wed Apr 09 2014 - 10:30:02 PDT
