[gmx-users] RE: why i cannot the long time md run

[Ing. Vojtěch Spiwok]

>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 
>
>nstxtcout=100
>nstxout=5000
>nstvout=5000
>dt=0.002
>nsteps=500000
>nstlog=200
>
>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?
>
>Thanks in advance,
>
>-- 
>xiaoyi li <xiaoyi at xray.bmc.uu.se>
>
Some unix instalations has filesize limit of 2GB
so this could be the case.
Check filesize limit by
ulimit -f
(in bash, I don't know how to do this in other shells).
if the answer is not "unlimited" type
ulimit -f unlimited
or call your clustermaster.
The precompiled version of gromacs could also have
such limit. I had this problem with Gamess US and I
fixed it by replacement of precompiled version by
one that I compiled myself. Gromacs could also crash
on Athlon without any reason (there are some mails
dealing with this problem in GMX archive).

Vojtech Spiwok
ICT Prague

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