VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Sep 25 2009 - 10:02:52 CDT

On Fri, 2009-09-25 at 16:25 +0200, Luca Gelisio wrote:
> Axel,
>
> reading the .pdb file works fine, though.
>
> Ok, I will do that... So, in this file there are all informations I
> need (that's atomic coordinates and atom type), right?
> Many thanks!

well, it is atomic "names" not "types" (VMD assumes you have a
biomolecule and there you have the 'label' that identifies an
atom in a residue and the force field type used to model it),
but based on what you answered to john, that should work for you.

if you will work more often with systems that large, you may
still consider switching to binary file formats, as the parsing
of > 10 millon atoms and coordinates in text format will take
a while. also the .pdb format throws away a lot of the precision
in the position data...

> Another quick question...
> Is there a place in which I can read something about this beautiful
> plugin? I mean, in which all features (for example rotation...) and
> how this works are explained...

the plugin is documented here.
http://www.ks.uiuc.edu/Research/vmd/plugins/solvate/

there also is a tutorial. if you want to learn how it works,
you probably need to read the plugin (script code). it is a
fairly trivial procedure, though, that just replicates a small
pre-equilibrated box of water molecules. FYI, this is meant_
to be used with and further equilibrated with MD simulations.
so the resulting structure tailored to let the MD start easily,
but not necessarily to give a good solvated structure right away.

BTW: if i am allowed some shameless self-advertisement. in case
you just want to build huge systems from a given unitcell of
coordinates, you may also give the "replicatemols" command a try
that is part of the topotools package:
http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/

cheers,
   axel.

> Thanks again,
>
> ciao,
> luca
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.