[gmx-users] A question on files "step*.pdb".

[Anton Feenstra]

Hwankyu Lee wrote:

> Dear. gmx-users,
> 
> I was running monolayer systems for 4ns without any problems, but suddenly I
> couldn't keep running them. When I checked my files, I could see a lot of
> step*.pdb files, and finally those files made the amount of my directory
> exceeded.

I've seen this happen a few times (and heard of others with the same problem).
It appears that your simulation should actually crash, that is, something went
wrong, but for some reason it keeps on going and writing out these .pdb files.
The way around this is to first delete all those .pdb files (you *don't* need
them), and then re-start from your .trr file. That is very easy to do, using
'tpbconv -f traj.trr -s topol.tpr -o restart.tpr' should produce a 'restart.tpr'
file, which you can give to mdrun. If the problem re-occurs, there is something
wrong in your monolayer system, e.g. close contacts or something else, which
you will have to fix somehow.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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