Your reply is very helpful to me. Thank you Alex! > -----Original Messages----- > From: Alex <nedoma...@gmail.com> > Sent Time: 2018-11-29 16:59:20 (Thursday) > To: gmx-us...@gromacs.org > Cc: > Subject: Re: [gmx-users] Re: Re: Re: How to fix graphite layers? > > > > My current plan is to divide the two atoms into two groups and set the > > peripheral atoms to the frozen group in mdp file. I am not sure what the > > interaction between the frozen and active groups is. If I need to generate > > top files for each of these two groups, how should I tell the 'hot > > graphite' to be binded to the frozen graphite adjacent to it? > > > I was talking about restraints, which are not the same as freezing > atoms. Once again, if the difference is not clear, please read the > manual and also maybe something more general about particle-based > simulations. In general, I believe that freezing atoms as part of a > finite-temperature simulation is completely wrong and should be avoided > as much as possible. > > Alex > -- > 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.
