[gmx-users] about mdrun errors!! again

David van der Spoel spoel at xray.bmc.uu.se
Tue Feb 18 13:54:51 CET 2003

On Tue, 2003-02-18 at 09:29, nanyu101 wrote:
> Dear Dr.David,
>   Thanks for your prompt reply.If my puzzle as you told that the large force was caused by the atoms being too close in the starting conformation.How can I fix it?I have already run EM and optimize it.
You have to find out what is causing the large forces. em tells you
which atom has the highest force. Genbox does not generate conformations
with overlapping atoms. Maybe you check the make hole program from
Graham Smith. (on gromacs website)

Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. 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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