> > Hello everyone! > > > > I am a new one of gromacs. When a simulation of protein in water is > > finished, > > should i first use the command of trjconv to remove pbc conditions(with > > nojump or mol), and then began analyze the new trajectory(rmsd, Rg and some > > other parameters)? Is the result believable without removing the pbc > > conditions or it is necessary for some specific calculations? > > > > Most Gromacs programs deal with PBC with no manipulation required, some do > not. > g_rms needs a properly processed trajectory. > > -Justin >
Thank you for your response! As you said, i also found the Rmsd by using -nojump or -mol is different from that without these commands. And i can not decide which one is more accurate. Furthermore, can you list some other parameters that need removed pbc conditions? such as SDF calculation ... -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
