[gmx-users] two questions on multiple simulations and stochastic dynamics

F.Hao at chem.rug.nl F.Hao at chem.rug.nl
Mon Apr 26 14:37:01 CEST 2004

Hi, all:
    I have two questions. 
1) I want to perform multiple simulation on one system and run them in 
parallel with gmx3.2.1. What I did is:
grompp -v -f md0.mdp -c pr.gro -p x.top -o topol0.tpr
grompp -v -f md1.mdp -c pr.gro -p x.top -o topol1.tpr
grompp -v -f md2.mdp -c pr.gro -p x.top -o topol2.tpr
grompp -v -f md3.mdp -c pr.gro -p x.top -o topol3.tpr

Then I sunmit this job to a cluster which had one processor on each node
by using "qsub myjob". myjob is a script:
#PBS -l nodes=4,walltime=240:00:00
cd working_directory/
mpirun -np 4 mdrun -multi -np 4 -s topol.tpr

It did produce four trajectories. But all four simulations were running 
on the first processor and leave the rest three nodes idle. Is it possible 
to let one subjob run on one of the four processors or I should do 
grompp -np 4 -v -f md0.mdp -c pr.gro -p x.top -o topol0.tpr ...?
Any hints will be sincerely appreciated!

2) I am using the stochastic integrator in gmx3.0.5. I notice that there 
is only the inverse friction constant used in mdp, does this mean that 
the friction force here is only related to the friction coefficient of
solvent molecules without considering the fraction of solute surface 
exposed to the solvent? In GROMOS96 package, the friction force is related 
to both. Since the friction coefficient of water is 91 (ps-1), what 
parameter should be set for tau_t as inverse friction constant in 
stochastic dynamics of biomolecules? Any help will be sincerely 


Best regards

Yours sincerely

Hao Fan :-)

Drs. Hao Fan                            email F.Hao at chem.rug.nl
Lab. of Biophysical Chemistry
University of Groningen
Nijenborgh 4                            9747 AG GRONINGEN
The Netherlands

Please don't call me on Friday due to the group meeting.

More information about the gromacs.org_gmx-users mailing list