RMSF is calculated for the atoms or groups you specify in your selection string. If you say, e.g. "protein and name CA" you will get all C alphas in the protein(s) in your system. See here http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html
On Thu, May 17, 2018 at 10:18 AM, Sampurna Mukherjee < sampurnamukherjeebiol...@gmail.com> wrote: > Hi gmx-users, > There are a few things I wanted to know: > > 1. For RMSF calculations, which atoms are used when I am calculating > RMSF for a group specified in the index? > 2. For gmx mdmat , for 2 protein chains taken together i.e using the > Protein group , "smallest distance between residue pairs" implies the > smallest distance over the trajectory between say the first and the 15th > residue.Yes? > 3. Which atoms are being considered for calculation of smallest > distances? > > > > Regards, > Sampurna > -- > 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. > -- Joe Jordan -- 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.