[gmx-users] It's spinning!

David van der Spoel spoel at xray.bmc.uu.se
Fri Dec 26 20:23:04 CET 2003

On Fri, 26 Dec 2003, [koi8-r] "Peter Mamonov[koi8-r] "  wrote:

>Dear Gromacs users,
>I've got a problem: while running molecular dynamics in vacuum using Berendsen thermostate my system (single aminoacid, I use it just for testing) starts rotating in spite of "comm_mode" parameter in MDP file is set to "angular". Could it be because of runnig Gromacs under Windows (I've downloaded Gromacs binaries for Win from www.gromacs.org)? Maybe there are some other parameters I should initialize? I would greatly appreciate receiving yor advices.

check your md.log 
Is the comm_mode really set to angular (or -1)?

>Dept. of Biophysics, Biological faculty, Moscow State University, Moscow, Russia.
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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