> > > Anupam Nath Jha wrote: >> Dear all >> >> I made an index file with 4 different groups for 4 different chains (since my >> protein is a tetramer) and then run >> >> g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out >> >> to get the rmsd between two different monomers from the same structure, >> it asked me two different groups and I gave 0 and 1. >> >> The output file is like this >> >> # g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o New >> # >> # g_rms is part of G R O M A C S: >> # >> # Grunge ROck MAChoS >> # >> @ title "RMSD" >> @ xaxis label "Time (ps)" >> @ yaxis label "RMSD (nm)" >> @TYPE xy >> @ subtitle "C-alpha_chain2 after lsq fit to C-alpha_chain1" >> 0.0000000 0.0000001 >> > > In the command you've given (with the same file for -s and -f), you're > computing > the RMSD at time zero, after fitting to the structure at time zero, so the > RMSD > must be zero.
but I am giving different groups (as chains). I am trying to get RMSD between two monomers in same structure so what's wrong in that.... - anupam >> >> so the rmsd = 0.0000001 >> >> whereas when I use online server it gives me 1.4. >> >> so what am I doing wrong? >> > > Then whatever you're giving the online server is different. The Gromacs > calculation seems to be correct. > > -Justin > >> regrads >> anupam >> >> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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/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/mailing_lists/users.php > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- Science is facts; just as houses are made of stone, so is science is made of facts; but a pile of stones is not a house, and a collection of facts is not necessarily science. Anupam Nath Jha Ph. D. Student Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-22932611 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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/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/mailing_lists/users.php