Re: simulating graphene sheets (with bonds across boundaries) with water

From: Axel Kohlmeyer (
Date: Tue Sep 15 2015 - 19:22:27 CDT

On Mon, Sep 14, 2015 at 7:59 AM, upayan baul <>

> 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.
> 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
> )
> which resulted in a configuration as shown (periodic) in:
> 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


> )
> which resulted in a configuration as shown in:
> 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
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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