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

David spoel at xray.bmc.uu.se
Wed Sep 3 19:46:01 CEST 2003

On Wed, 2003-09-03 at 18:38, 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 
> 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?

Probably the 2gb is the problem. Have you checked the log file whether
these settings have made it into the tpr file (and hence in the md.log

> Thanks in advance,
Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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