From: Javier Goicochea (
Date: Fri Jan 16 2009 - 02:10:19 CST


Thank you for your comments. As you mention, some potentials for Quartz
involve three body interactions, however, recently a two body potential for
NAMD was published. I was hopping to use psfgen or writepsf to create the
PSF file, but since I am only interested in the ANGLE and DIHEDRAL sections
I will continue working with my own code to create it for my geometries.

I have noticed that the creation of angles and dihedrals in VMD is quite
fast. Do you know the location of the code that performs these calculations
in VMD? I have search a bit the VMD code, but I could not find it. I will
post a new message in the mailing list but this.

Regards, Javier

On Thu, Jan 15, 2009 at 9:06 PM, Axel Kohlmeyer <
> wrote:

> On Thu, 15 Jan 2009, Javier Goicochea wrote:
> JG> Hi all,
> hi javier,
> JG> I am trying to use correctly topology files. The molecular system I am
> JG> building is composed by different substances: solids and liquids, for
> JG> example (but not limited to) Quartz and Water or Silicone. So far, I
> can
> JG> create PDB files for the different geometries and substances to be
> studied.
> JG> However, I do not have the topology files for Quartz, nor for the other
> JG> solids I want also to study. I am basically interested in using psfgen
> in
> JG> VMD to create the PSF file, but I need the topology file.
> there is a topology generation tutorial on the TCBG homepage,
> but i don't think this is the proper strategy to address your problem.
> the first and most important question that you have to address,
> it what kind of interaction potential are you going to be using for
> your quartz part of the system and how many of those atoms would
> actually be moving. for example, if you need some 3-body potentials,
> you will have to do some programming first, IIRC.
> then i would recommend to write a code that generates the .psf
> file for that crystal part of your system directly alongside
> the .pdb file and then you are fine. for the rest of processing
> with psfgen you can just read in the existing coordinates and
> topology and psfgen should honor it.
> JG> At this point, I have been trying to understand the structure / format
> of
> JG> the topology file and I have managed to create a simple (initial)
> version of
> JG> the topology file for Quartz. This topology file can create the PSF
> file,
> JG> with bonds, angles and dihedrals.
> the CHARMM type topology (actually "residue template file" would be a
> better word) that you want to write implicitly assumes that you want
> to build some peptide like polymer. it doesn't work for crystals.
> trying to make it work would be much more effort than just writing
> your .psf file directly.
> but let me reiterate, the most serious problem would be to identify
> the force field parameters for quartz, and for all i remember from
> what somebody told me a long time ago, you cannot do that well
> without 3-body interactions...
> cheers,
> axel.
> --
> =======================================================================
> Axel Kohlmeyer
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.