From: Axel Kohlmeyer (
Date: Thu Apr 28 2011 - 10:01:18 CDT

On Thu, Apr 28, 2011 at 2:38 AM, kanchi subbarao rao <> wrote:
> hi to all
>  i am a new user to vmd and namd . i want to run simulation on a composite
> system of lipid-bilayer and graphene.for that i build my system in i
> had pdb file of that to run my simulation in namd by using charmm
> force field,i need topology file for my system.i do not know how to get
> topology file for my system.

for the lipids, you can probably proceed with the standard procedure as outlined
in the NAMD and topology tutorials. graphene is a bit trickier, since
it is a bit
difficult to write a topology for that. however, this is a problem,
that the topotools
plugin was written to address.

if you construct the graphene with the nanotube builder GUI in VMD, it
will automatically
assign the atom type of a benzene atom to all carbons and generate all bond,
angles, dihedrals and impropers for you. so all that is left is to
write out a .psf and .pdb
file and then at a later stage merge those with the lipid bilayer.

for non-CHARMM systems, or MD codes other than NAMD, some extra work
is required to get to the same answer.


> please help me ,

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.