Hi Vitaly Unfortunately, the paper does not mention anything about whether the forcefields for graphene were taken from OPLS or AMBER. If I could get the topology file (even for part of) the graphene , it would have been very helpful. I could have replicated and improvised the topology files for the graphene size I am interested in. Jagannath
On Fri, Jan 15, 2016 at 6:14 AM, VITALY V. CHABAN <vvcha...@gmail.com> wrote: > The force constants were either from OPLS or from AMBER (which of these is > referenced in the paper?) > > > > On Thu, Jan 14, 2016 at 5:40 PM, jagannath mondal <jm3...@columbia.edu> > wrote: > > > Hi Vitaly > > Thanks for pointing to the paper. > > Based on the paper, "GR was simulated as a non-polarizable assembly of > > carbon atoms linked by harmonic potentials with the following bonded > > parameters: distance (C–C)= 1.41 nm, angle (C–C–C) = 120 , dihedral > (C–C–C > > –C) =0 " > > Can you please specify what were the values of force-constant used for > > bonds, angle and dihedrals ? > > Jagannath > > > > > > > > On Thu, Jan 14, 2016 at 6:53 PM, VITALY V. CHABAN <vvcha...@gmail.com> > > wrote: > > > >> By using high force constants for all bonded terms. > >> > >> An ideally planar graphene in the solution/dispersion is an unphysical > >> model though. You must read literature for further insights: > >> > >> > >> > http://pubs.rsc.org/en/content/articlelanding/2015/ra/c5ra16857k#!divAbstract > >> > >> > >> > >> > >> > >> > >> On Thu, Jan 14, 2016 at 5:13 AM, jagannath mondal <jm3...@columbia.edu> > >> wrote: > >> > >> > Hi > >> > > >> > Which restraints can one use to maintain planarity of graphene > sheets > >> > while performing MD simulations of their association ? I guess > >> > flat-bottommed restraints will not work. > >> > > >> > Jagannath > >> > -- > >> > 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. > -- 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.