[gmx-users] how to maintain planarity of graphene sheet

[jagannath mondal]

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 <vvchaban at 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 <jm3745 at 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 <vvchaban at 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 <jm3745 at 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
> >> > --
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