[gmx-users] RMSD

[felmerino at uchile.cl]

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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