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

From: Abhishek TYAGI (
Date: Mon Sep 14 2015 - 19:28:04 CDT

Dear Upayan,

In your work you may try fixing the graphene sheet i hope you know how to do it or you may restrain them, and for the error, it seems like that your box is small, try to use bigger pbc than your original dimensions, have a look on PME too.



Abhishek Tyagi

PhD Student

Chemical and Biomolecular Engineering

Hong Kong University of Science and Technology

Clear Water Bay, Hong Kong

From: <> on behalf of upayan baul <>
Sent: Monday, September 14, 2015 7:59 PM
To: Namd Mailing List
Subject: namd-l: simulating graphene sheets (with bonds across boundaries) with water

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 )
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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