simulating graphene sheets (with bonds across boundaries) with water

From: upayan baul (
Date: Mon Sep 14 2015 - 06:59:00 CDT

Dear NAMD users,

Sorry for the long mail. I wished to let you know the things I have already

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
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,
and nonbonded interactions from CHARMM protein parameters (par_all22_prot).
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 )
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

Thanking you,
S.R.F., Physics

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