[gmx-developers] CVS implementation of REMD

Ken Rotondi ksr at chemistry.umass.edu
Thu Jun 2 22:43:04 CEST 2005

Hello all,

Okay, I've been wearing another hat for the last few days. It would 
appear that I've figured this out and wanted to post for the general 


I'm running the VERSION 3.3_beta_20050202 CVS code:

I was worried that trying to simulate only 2 replicas was somehow 
bollocksing up the works, so I created 4 .tpr files named (in 
increasing temperature) topol0.tpr, topol1.tpr, topol2.tpr, & 
topol3.tpr using the:

grompp -f 1.mdp -po 1out.mdp -c md8.gro -p p39a.top -o topol0.tpr


mpirun -np 4 mdrun -multi -replex 200 -reseed 1

command would appear to start a REMD run (4 sets of "starting mdrun 
'protein in water' tags appear).

Next question, are the acceptance ratios for exchange part of the 
standard output? If not how could one extract them (they are important, 
so I assume that they would be part of the output)?

Many thanks for the persistent help,


On May 27, 2005, at 5:09 AM, hessb at mpip-mainz.mpg.de wrote:

> Quoting Ken Rotondi <ksr at chemistry.umass.edu>:
>> Thanks for the suggestions. I'm probably doing more than two things
>> incorrectly...
>> Okay, I used grompp to generate sequentially numbered .tpr files 
>> using:
>> grompp -v -f 1.mdp -po 1out.mdp -c md8.gro -p p39a.top -o topol0.tpr
>> grompp -v -f 2.mdp -po 2out.mdp -c md8.gro -p p39a.top -o topol1.tpr
>> where 1.mdp and 2.mdp are .mdp files for adjacent temperatures in a
>> REMD analysis I am setting up.
>> Then I ran mdrun:
>> mdrun -v -multi -np 2 -replex 20 -s topol.tpr
>> Response?
>> Can not open file:
>> topol.tpr
> Strange.
> This should work.
> There has been a problem like this half year ago.
> But in the current CVS this should work fine.
> Many people use the CVS REMD code without problems.
> Are you using recent CVS code?
> Berk.

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