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.sant...@ibs.fr Fecha: 15-nov-2011 10:18 Para: "Discussion list for GROMACS users"<gmx-users@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 _________________________________________________________ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html
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