[gmx-users] translation problem in rmsd of dynamic run
David van der Spoel
spoel at xray.bmc.uu.se
Wed Oct 22 16:22:01 CEST 2003
On Wed, 2003-10-22 at 15:41, Madhuri Agashe wrote:
> I have a MD simulation run of 600ps. To analyze the result, I ran the
> g_rms command.
> What has happened though is that the structure has not changed much,
> but has translated along the Z axis after around 300ps. Due to this
> the g_rms output does not reflect the correct picture of the structure
> remaining unchanged after the dynamics run.
Normally g_rms should take care of that, unless you turn off the
fitting. Have you done that?
> Is there an option (or another command) so that the translation can be
> ignored and just the structural changes reflected in the RMS output?
> Madhuri Agashe
> Graduate Research Assistant,
> Dept. of Bioengineering,
> Clemson University,
> Clemson, SC 29631
> Phone: 864-653-4230 (resi)
> 864-656-1352 (off.)
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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