What I see in xvg file is as below: # g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg # # g_rms is part of G R O M A C S: # # Gromacs Runs On Most of All Computer Systems # @ title "RMSD" @ xaxis label "Time (ps)" @ yaxis label "RMSD (nm)" @TYPE xy @ subtitle "Protein after lsq fit to Protein" -1.0000000 0.2510229
I though that -1 is the ref value and the other is the relative RMSD for 2.pdb. Is this -1 should be positive? What is this -1? Would you give me any suggestions please? Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Wednesday, January 23, 2013 9:36 PM Subject: Re: [gmx-users] RMSD On 1/23/13 12:48 PM, Shima Arasteh wrote: > 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? > The RMSD value should be positive, so I don't know how you get -1. Your approach does not seem very sound - a structure does not have an absolute RMSD value; it has an RMSD value relative to a reference structure, which must be some sort of meaningful comparison or else you're not really measuring anything useful. -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 -- 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
