[gmx-users] why i cannot the long time md run
feenstra at chem.vu.nl
Thu Sep 4 09:34:01 CEST 2003
xiaoyi li wrote:
> To whom it concerns,
> I am trying to run a long time MD simulation on a complicated system
> composed of two axt molecules and two proteins with Gromacs. I set
> in the .mdp file to get the 1000ps result. But the real output result is
> only 110s. The size of the output file are:
> .log 2147483647
> .trr 13120992
> .tpr 6588032
> Is it because of the size limit of the output file? what's the size
> limit of all the output files? what should i do then? If not, why I
> cannot get the right long time run?
I don't know why your output is not complete, but I would suggest writing
less often, especially to the logfile. All energy values are also stored
in the energy file (and much more compact). I set nstlog to 5000 or 10000.
(saves you a factor 20-50!) Also, you are writing 5 frames per ps to your
.xtc trajectory, that is a lot. I usually only write 1 frame per ps (saves
you a factor of 5).
Did you check the logfile and/or screen output of mdrun for any clues why
you simulation has stopped?
| | |
| _ _ ___,| 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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