The values are OK, you obtain a value of RMSD of 0.2510229 . The value -1 refers time, and it is because you do not have a trajectory. You are comparing only two .pdb structures, so it is consistent that you obtain only one value, as you do not have more than one frame to compare. Regards Flor Dra.M.Florencia Martini Cátedra de Farmacotecnia II Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Junín 956 6º (1113) TE: 54 011 4964-8273
________________________________ De: Shima Arasteh <shima_arasteh2...@yahoo.com> Para: Discussion list for GROMACS users <gmx-users@gromacs.org> Enviado: miércoles, 23 de enero de 2013 16:14 Asunto: Re: [gmx-users] RMSD 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 -- 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
