[gmx-users] understanding the output of REMD
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 28 03:23:58 CEST 2011
sreelakshmi ramesh wrote:
> after having enough exchanges how to follow the temp trajectory of each
> replica in REMD ? I tried to make it out from edr file of each
> replica.looks like replica at a particular temp remains almost at a same
> temp throughout the simulation and does not visit all the other
> tempratures.any help please.
>
>
Trajectories and energy files are ensemble-continuous. Use the demux.pl script
to demultiplex the trajectories and produce temperature evolution over time.
-Justin
> Regards,
> sree.
>
> On Wed, Jul 27, 2011 at 4:58 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> sreelakshmi ramesh wrote:
>
> dear all ,
> I am new to ReMD simulations.And i done a trial run of 100 ps
> for 7 replicas . if i view the log file for output i get
> something like this for every replica
> for one of the replica the log file looks like this
>
> Replica exchange at step 1000 time 2
> Repl 0 <-> 1 dE = 6.793e+02 dpV = 0.000e+00 d = 6.793e+02
> Repl ex 0 1 2 3 4 5 6
> Repl pr .00 .00 .00 Replica exchange at step
> 2000 time 4
> Repl ex 0 1 2 3 4 5 6
> Repl pr .00 .00 .00
> Replica exchange at step 3000 time 6
> Repl 0 <-> 1 dE = 6.790e+02 dpV = 0.000e+00 d = 6.790e+02
> Repl ex 0 1 2 3 4 5 6
> Repl pr .00 .00 .00 Replica exchange at step
> 4000 time 8
> Repl ex 0 1 2 3 4 5 6
> Repl pr .00 .00 .00
> Replica exchange at step 5000 time 10
> Repl 0 <-> 1 dE = 6.874e+02 dpV = 0.000e+00 d = 6.874e+02
> Repl ex 0 1 2 3 4 5 6
> Repl pr .00 .00 .00 Replica exchange at step
> 6000 time 12
> Repl ex 0 1 2 3 4 5 6
> Repl pr .00 .00 .00
> Replica exchange at step 7000 time 14
> Repl 0 <-> 1 dE = 6.535e+02 dpV = 0.000e+00 d = 6.535e+02
> Repl ex 0 1 2 3 4 5 6
> Repl pr .00 .00 .00
> i had attached only few lines of log file.can any one tel me
> how to understand the output.
>
>
> I assume you've seen the following?
>
> http://www.gromacs.org/__Documentation/How-tos/REMD#__Understanding_REMD-related___Output
> <http://www.gromacs.org/Documentation/How-tos/REMD#Understanding_REMD-related_Output>
>
> Listed are the exchange probabilities between neighboring replicas.
> Your results indicate that your systems are not exchanging (e.g.
> probability is zero).
>
> -Justin
>
> --
> ==============================__==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================__==========
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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