[gmx-users] understanding the output of REMD

[Justin A. Lemkul]

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

Listed are the exchange probabilities between neighboring replicas.  Your 
results indicate that your systems are not exchanging (e.g. probability is zero).

-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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