[gmx-developers] RasMol on Debian

David van der Spoel spoel at xray.bmc.uu.se
Mon Nov 21 14:30:55 CET 2005

On Mon, 2005-11-21 at 13:05 +0000, Michael Bajomo wrote:
> Sir,
> This is not a gromacs developer question but I am desperate and you
> are the only one that can help me. I learning to use gromacs as part
> on my project and I ran the Ribonuclease s-peptide tutorial on the
> gromacs website ( www.gromacs.org). I modified the .mdp file so it
> runs for 1ns. When I check pressure using g_energy the average is
> 0.85bar but the RMSD is 345bar. The .mdp file specifies 1bar and
> berendsen P-coupling. I don't know what I have done wrong. Any advice
> will be appreciated.
The topic of this mail is a bit misplaced.

Otherwise the result is correct. The pressure does fluctuate that much.

> Thank you and kindest regards
> Michael
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David van der Spoel, PhD, Assoc. 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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