[gmx-users] RMSD

[shahid nayeem]

Thanks. But in timeline plugin of VMD I am able to measure RMSD with
respect to one of the frame of trajectory and I am interested to measure
RMSD with respect to another molecule. I am trying to measure RMSD of
trajectory frames with respect to Bound and unbound configuration of
molecule so that I can compare side chain configuration of trajectory with
bound and unbound sidechain configuration.  Please help.
Shahid Nayeem

On Tue, Nov 15, 2011 at 7:02 PM, felmerino at uchile.cl <felmerino at uchile.cl>wrote:

> In any case, if you really want to see flexibility then you need RMSF and
> not RMSD as the later will only tell you about how similar is the
> configuration of a sidechain compared to a reference frame. If that is
> still what you want i think VMD has a tool for that in the timeline plugin.
>
>
>
> regards
>
>
>
> Felipe
>
> ----Mensaje original----
> De: gianluca.santoni at ibs.fr
> Fecha: 15-nov-2011 10:18
> Para: "Discussion list for GROMACS users"<gmx-users at gromacs.org>
> Asunto: Re: [gmx-users] RMSD
>
>
> On 11/15/11 8:23 PM, shahid nayeem wrote:
>
> Dear all
> I am interested to get contour plot of residue RMSD vs time graph. I want
> to get the flexible and rigid regions of protein chain during simulation.
> g_rmsf does not gives me this plot.
> Please help
> shahid Nayeem
>
>
>
> Try g_rmsf -res , it could be useful, maybe.
>
> --
> Gianluca Santoni,
> Institut de Biologie Structurale
> 41 rue Horowitz
> Grenoble
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