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

[VITALY V. CHABAN]

I checked. They are from AMBER.



On Fri, Jan 15, 2016 at 5:50 AM, jagannath mondal <jm3745 at columbia.edu>
wrote:

> 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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>
>