The acceptance rate seems artificially high. It was not supposed to be that high. I'm pretty sure something weird is going on, and I need to run down what is going on, or I won't be able to trust the results (otherwise, I would just run fewer replicas and save myself the simulation time). Exchange is attempted every 500 MD steps.
Chris Thiebaut
Graduate Student
Purdue University
----- Original Message -----
From: "Brian Radak" <radak004.umn.edu>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Wednesday, April 9, 2014 1:29:48 PM
Subject: Re: [AMBER] Really Weird Problem with Replica Exchange
I don't really do T-REMD too much, but isn't the velocity scaling a
temperature dependent factor that goes as sqrt(T1/T2) or something? For
such closely spaced temperatures, that could very easily be 1.00. I could
be totally wrong on that though.
Another relevant question may be what is your exchange attempt frequency?
Some may disagree with me, but I would think that having a high acceptance
rate *and* a high attempt frequency would be a bad thing and potentially
lead to weird results.
Regards,
Brian
On Wed, Apr 9, 2014 at 1:05 PM, Christopher A Thiebaut
<cthieba.purdue.edu>wrote:
> 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
> >
> >
> ---------------------------------------------------------------------------------------
> > _______________________________________________
> > 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
>
--
================================ 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.
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Received on Wed Apr 09 2014 - 11:00:03 PDT
