[gmx-developers] CVS implementation of REMD

Ken Rotondi ksr at chemistry.umass.edu
Wed May 25 15:17:42 CEST 2005

Thanks for the suggestions. I'm probably doing more than two things 

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


Can not open file:

So I tried

mdrun -v -multi -np 2 -replex 20

same result.

A nice, simple, example of grompp and mdrun statements to achieve REMD 
would help a lot and likely avoid lots of back and forth.

Sorry to keep pestering,


On May 25, 2005, at 3:23 AM, Berk Hess wrote:

> Ken Rotondi wrote:
>> Hello all,
>> I'm having a bear of a time getting started with REMD in the CVS code.
>> I have succeeded in compiling the CVS code with mpi support.
>> I've made two .tpr files for two adjacent temperatures, named 
>> topol0.tpr and topol1.tpr  as an initial test, using:
>> grompp -v -np 2 -f 1.mdp -po 1out.mdp -c md8.gro -p p39a.top -o 
>> topol0.tpr
>> To start mdrun:
>> mdrun -v -multi -np 2 -replex 20 -s topol*.tpr -o
>> Fatal error: run input file topol0.tpr was made for 2 nodes, while 
>> mdrun expected it to be for 1 nodes
>> mpirun -np2 mdrun -multi -v -np 2 -replex 20 -s topol*.tpr -o
>> returns the mpirun man page
>> This is a single processor box, but I don't see that effecting the 
>> number of processes that can be run (just the speed with which they 
>> will finish).
>> What am I doing wrong?
>> How are the input and output files specified in the mdrun command 
>> (using a * wildcard)?
>> Unfortunately the CVS manual does not include the Appendix with the 
>> manual pages in it, however, mdrun -h should provide the same 
>> information.
> mdrun -h gives the required help.
> The -replex help refers to -multi, which in turn says:
> With -multi multiple systems are simulated in parallel. As many 
> (single node)
> input files are required as the number of nodes. The node number is 
> appended
> to each input and output filename, for instance topol.tpr becomes 
> topol0.tpr,
> topol1.tpr etc. The main use of this option is for NMR refinement: when
> distance or orientation restraints are present these can be ensemble 
> averaged
> over all the systems.
> So you did two things wrong.
> The tpr files should be single processor (grompp -np 1).
> And you do not need to specify -s (or specify -s topol.tpr).
> Maybe we should clarify the second point in the help.
> Berk.
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