[gmx-users] RMSD

felmerino at uchile.cl felmerino at uchile.cl
Tue Nov 15 14:32:16 CET 2011

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.




----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
Please avoid sending me Word or PowerPoint attachments.
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