Hi, On Tue., 16 Jul. 2019, 10:32 ehsan shahini, <[email protected]> wrote:
> Dear all, > > 1. I need to restrain a small molecule in a region (cylindrical) and I want > to restrain all of its atoms in that region. The best tool is flat-bottomed > restrain but it only restrains individual atoms in their corresponding > regions and not all the atoms in a single region. > > Hence, if I want to change the main code related to flat-bottomed where can > I find it? > No need. Use grompp -r to restrain the position of each atom to the same position that is the centre of the desired region. Another question > > 2. Can we introduce virtual sites in Gromacs which are static and defined > by the user via the XYZ coordinates of them? > No, but you can have frozen particles that have whatever interactions that you choose. Mark Kind regards, > > Ehsan > -- > 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 [email protected]. > -- 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 [email protected].
