I want to to calculate Rg of whole protein in the simulation box at a time not the individual chains. And for this I have selected Rg for "C-alpha" atoms plus "-nmol 3" .
Thank You, Sundari On Mon, Apr 8, 2019 at 2:50 PM Soham Sarkar <soham9...@gmail.com> wrote: > What do you want? > Do you want to calculate the radius of gyration of the three chain at a > time? > If so then make a index of these protein chains together and calculate rg > by selecting it. If not then calculate the chain's rg individually. > -Soham > > On Mon, 8 Apr 2019, 2:36 pm Sundari, <sundi6...@gmail.com> wrote: > > > Dear Gromacs users, > > > > Can anyone explain about -nmol (number of molecules ) option in gmx > gyrate > > tool. According to me I have 3 peptide chains in my simulation box and I > am > > using " -nmol 3". > > Is it correct what I have used for this option? > > > > Regards > > Sundari > > -- > > 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. > > > -- > 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. > -- 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.