[gmx-users] understanding the output of REMD

[Justin A. Lemkul]

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

========================================