You can probably use gmx solvate for this with the frame at the end of 50 ns as input cp and a box of the new molecules as cs or possibly genion. We also have a tool for building simulation systems with small molecules called DruGUI http://prody.csb.pitt.edu/drugui/ although I don't know how you would convert the topology from NAMD .psf to Gromacs .top format.
Best wishes James On Tue, Jul 10, 2018 at 7:21 AM, Soham Sarkar <soham9...@gmail.com> wrote: > Dear all, > I am planning to do a simulation where after 50ns of simulation I want to > add some other chemicals in the system and continue it for another 50ns, so > that I can have the effect of that chemicals exclusively before and after > adding it to the system.Is it at all possible? If yes please tell me the > protocol/ commands or give me some references where this type of simulation > is used. Thanks in advance. > -Soham > -- > 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.