I want to find the structure with the lowest RMSD, so I think it does not make different to set any of pdb files as the ref structure. I made an attempt and got the RMSD regarding the first pdb file. The RMSD relative to -1 for the ref structure, is written in xvg file. Is my approach logically correct?
Thanks for your suggestions. Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Wednesday, January 23, 2013 7:20 PM Subject: Re: [gmx-users] RMSD On 1/23/13 10:38 AM, Shima Arasteh wrote: > > > Hi, > > Is it possible to get RMSD of 10 different pdb files by GROMACS? Relative to what? Each other? Some universal reference? > g_rms may help? > That, or g_confrms, depending on what you're actually trying to measure. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
