[gmx-users] -res option in g_rmsf

Dawid das addiw7 at googlemail.com
Mon Sep 1 15:06:11 CEST 2014


Okay, so if it contains both backbone and sidechain residues, then both of
them are taken to calculate RMSF.

Thanks.


2014-09-01 13:57 GMT+01:00 Tsjerk Wassenaar <tsjerkw at gmail.com>:

> Hi Dawid,
>
> That depends on your index group.
>
> Cheers,
>
> Tsjerk
>
>
> On Mon, Sep 1, 2014 at 2:51 PM, Dawid das <addiw7 at googlemail.com> wrote:
>
> > Dear Gromacs experts,
> >
> > Let's say I calculate RMSF for each residue (-res), using Protein group
> > from index file. Now what atoms are actually taken for a residue? Only
> > sidechain atoms or sidechain atoms plus backbone ones?
> >
> > Best wishes,
> >
> > Dawid Grabarek
> > --
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
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