[gmx-users] Re: memory problems...

[Anton Feenstra]

Giorgos Karvounis wrote:
> 
> Dear Sir or Madam,
> 
> My name is George and i am a new user of Gromacs. My problem is that ,
> if i let a small peptide run for 500 ps, e.g 20 residues polyanaline,
> the programs runs out of memory because the pr.trr file gets huge! What
> can i do about that? How can i recover the simulation?

First, you should really post these type of questions to the Gromacs
mailing list. That way more people will read it, so you have a better
chance for a quick answer, and the answer will be available in the
list archives for other people to find...

No to your question: if you say memory, I must assume you mean
diskspace,
since you mention the .trr file. Is that correct? That then probably
means that you have set the nstxout, nstvout and/or nstfout flags in
your .mdp file to 1 or so, so that at every time step a frame will
be written to your trajectory file. That is usually not necessary, in
stead it should be sufficient to write to .xtc (which uses much less
diskspace) with nstxtcout every 1 ps or so (500 steps at 0.002 ps time
step), and write to .trr with nstxout and nstvout every 10 ps or so
(5000 steps). Writing forces is hardly ever useful at all. Also, using
xtcgrps you can set which groups will be written to your .xtc file, e.g.
you might only need your protein and not your water.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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