From: upayan baul (margheritan22_at_gmail.com)
Date: Wed Sep 16 2015 - 05:40:38 CDT
Thank you for your response!
Regards,
Upayan
On Wed, Sep 16, 2015 at 5:52 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
>
> On Mon, Sep 14, 2015 at 7:59 AM, upayan baul <margheritan22_at_gmail.com>
> wrote:
>
>> Dear NAMD users,
>>
>> Sorry for the long mail. I wished to let you know the things I have
>> already tried.
>>
>> I wish to simulate a system with stacked graphene sheets (with bonds
>> across
>> boundaries in XY) in water in an NPT ensemble. The initial configuration
>> of the
>> system is shown in.
>>
>> https://www.imsc.res.in/~upayanb/graphene_namd/no_improper/graphene_wat_init.jpg
>>
>> As an ideal test case, I wish to retain the planarity of the graphene
>> sheets to as great a
>> degree as possible.
>>
>> I am using atom type CA and corresponding parameters for bond, angle,
>> dihedral
>> and nonbonded interactions from CHARMM protein parameters
>> (par_all22_prot). I
>> have tried small simulations
>>
>> without impropers : (based on Kenno's suggestion that impropers only
>> over-rigidify 6
>> membered ring structures
>> http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=33962
>> )
>> which resulted in a configuration as shown (periodic) in:
>>
>> https://www.imsc.res.in/~upayanb/graphene_namd/no_improper/graphene_wat_fin.jpg
>>
>> with impropers: (based on Axel's suggestion (though this might be for the
>> finite-sheet case,
>> I might have misunderstood) to include impropers for planarity
>>
>
> FYI, if you are using CHARMM parameters, you should not use impropers.
> CHARMM dihedrals should be sufficient to give the right planarity.
>
> i am not sure whether the ondulations you see are unphysical for a LJ
> potential with spherical cutoff, but the easiest way that comes to my mind
> to keep those graphene sheets in place would be using the FixedAtoms
> command.
>
> axel.
>
>
>
>
>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/19410.html )
>> which resulted in a configuration as shown in:
>>
>> https://www.imsc.res.in/~upayanb/graphene_namd/with_improper/graphene_wat_fin_impropers.jpg
>> in which I have used an additional improper interaction of
>> !atom types Kpsi psi0
>> CA CA CA CA 10.0 0 0.00
>>
>> Neither of the two cases are resulting in highly planar structures.
>> Increasing Kpsi is resulting
>> in more puckered structures (for Kpsi > 20, the simulations are crashing
>> with statements like
>> ERROR: Atoms moving too fast; simulation has become unstable (3 atoms on
>> patch 1 pe 0).
>>
>> How can I obtain a more planar configuration for graphene? I have tried
>> fixed atom simulations.
>> In NPT, without constant area such simulations crash owing to fixed atom
>> at boundaries. With
>> constant area, the system expands in the Z- direction, causing the water
>> to move away from the
>> surface.
>>
>> Thanking you,
>> Upayan
>> S.R.F., Physics
>> IMSc
>>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
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