[gmx-users] translation problem in rmsd of dynamic run

Madhuri Agashe magashe at CLEMSON.EDU
Wed Oct 22 17:00:02 CEST 2003

I am not sure how to turn on/off the fitting.
Is this taken care of by -fit?
If so, I had not used it. Is the default value for this 'yes'? I had not
specified anything.
Should I do that?

-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
On Behalf Of David van der Spoel
Sent: Wednesday, October 22, 2003 10:21 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] translation problem in rmsd of dynamic run

On Wed, 2003-10-22 at 15:41, Madhuri Agashe wrote:
> Hi,
> 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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