[gmx-users] A few general questions on Gromacs

[Stéphane Téletchéa]

Corina Stratan a écrit :
> Hi,
> 
> I would like to thank you and David for the answers. By "multiple 
> programs", I meant batch scripts that contain other 
> preprocessing/postprocessing programs besides mdrun  (like grompp, 
> pdb2gmx,...) - so this would be a case in which the processing is done 
> in multiple steps. I asked this because we're especially interested in 
> multi-step processes (workflows); and in the Gromacs tutorials most of 
> the examples are like this (some other programs are invoked before and 
> after mdrun).
> 
> Thanks again!
> Corina
> 

Your mileage may depend on your cpu availability, for instance, you can 
do in one batch job either:
- grompp+mdrun
- grompp+mdrun(em1), grompp+mdrun(em2), grompp+mdrun(pr1), ...

Ideally, one would do (in order to share ressources:
- 1 batch file containing all the "setup" steps (those are quite "rapid" 
usually), namely energy minimisation and positional restraints
- this batch job launches the next step (after some verification if you 
need to) automatically, thus *chaining* them
- 1 batch file for the "production" (the one you'll use for your 
analyses/statistics), which can itself be splitted.

That would be:
batch-setup --
              |
              ->batch-production1 (--
                                    |
                                    ->batch-production2...n).

The more you chain, the more you'll need to validate your steps :-)

For the benchmark in itself, you can easily generate a *big* box of 
water but you'll not really benchmark the system even with such a big 
system if your interconnection is not fast enough (i.e. you have fast 
network *and* low latency, gigabit for instance is not very efficient 
for a good scaling).

Cheers,
Stéphane

-- 
Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901