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, felmer...@uchile.cl <felmer...@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.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 > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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