From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Sep 15 2015 - 19:22:27 CDT
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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