Re: Generating topology files for crystalline materials

From: Axel Kohlmeyer (
Date: Sun Feb 10 2013 - 12:22:09 CST

On Sun, Feb 10, 2013 at 7:05 PM, FX <> wrote:
> Dear NAMD list,
> I'm trying to get a NAMD simulation running for an organic-inorganic crystalline material. I already have a forcefield for my system, and already run some MD using other codes. I'm now trying to create inputs file for an NAMD simulation, but I am at loss how to create the topology file. I've read the tutorials (both the generic tutorial and the advanced "topology files" tutorial), but they only cover biological systems made of a series of residues.
> In my case, the entire unit cell is made of only one molecule, extending in 3D through periodic boundary conditions. So, I'm wondering: what is the procedure I should follow to create this topology file?

since psfgen more or less assumes that your system can be represented
by "templates" which are either standalone or connected in a specific
way (like peptides are formed from a chain of amino acids), you'd have
to come up with some way to generate that structure separately and
then merge it with the organic part.

the molfile plugin API now also supports writing out topology
information, so you can generate the topology information from VMD
scripting. this can be tedious and error prone, so it would be
beneficial to write some scripted tools for that. the topotools
plugin, for example provides a "middleware" that can automate a large
part of the process. check out:

you'll have to come up with a smart way to add the bonds that wrap
around periodic boundaries and i would be curious to learn, if the
automatic derivation of topological angles and dihedrals will work
correctly in those cases (never had a chance to try it on a real world

it may be simpler to build the topology information direction, since
you know your structure and i assume there are some simple rules to

good luck,

> Thanks in advance for any help or resource you can point me to!
> Sincerely,
> François-Xavier Coudert

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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