Message: 5 Date: Wed, 8 May 2013 08:25:33 +0200 From: Tsjerk Wassenaar <tsje...@gmail.com> Subject: Re: [gmx-users] PCA_RMS fluctuation per residue? To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <CABzE1Sj6vTMwRSFQo3BUpqtxCuJpcZVnQMd=suab52eb9nf...@mail.gmail.com> Content-Type: text/plain; charset=UTF-8
Thank you for the reply Tsjerk. Could you tell me how i can visualize the motion s of eigenvectors ? I read from somewhere, In order to reveal the 3d motions via VMD/chimera have to add the msd value in filtered pdb file of eigenvector? If that so, how it can be done? Hi Rajiv, Square the values, sum them per residue and take the square root. Cheers, Tsjerk On May 8, 2013 7:24 AM, "���������������" <ra...@kaist.ac.kr> wrote: Dear gmx users, I've done covariance matrix for backbone of protein using g_covar command. Also, can able to plot all projections through g_anaeig. However, I could only able to do -rmsf: plot the RMS fluctuation per atom of eigenvectors BUT i wants to do them per residue? How can i achieve this? In manual it shows -filt: command filter the trajectory to show only the motion along eigenvectors. How i do visualize this kind of motions?
-- 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
