If you aren't adding anything too big, or to much of them, then take the final frame, use gmx insert-molecules (probably with a reduced vdw radius so they fit in) to put the additional molecule(s) in, perform standard pre production run energy minimisation etc, then off it goes again.
Why can't you start two separate systems, one without, and one with? That would be a more robust way to do it. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. On Tue, 10 Jul 2018 at 21:22, 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.