VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 25 2009 - 11:03:47 CDT

Hi,
  I just wanted to amplify Axel's warning that with the PDB format,
you will lose a lot of precision in your atom coordinates with structures
of this size. Even though you might be able to read the PDB file generated
by this process, the coordinates at the corners will have much lower precision
than those near the origin. Technically the PDB was only ever intended for
structures containing up to 99,999 atoms, and to go beyond that is no longer
a legal PDB file, though we do this all the time by virtue of ignoring the
atom index fields.

For others reading this discussion, another thing to note is that
large coarse grain models will also break the normal file formats
if you get CG beads/particles with very large masses or other
attributes that overflow the PDB atom field widths.
The next version of VMD will hopefully include the (currently experimental)
new version of psfgen that allows writing to binary file formats that
don't have these problems.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Sep 25, 2009 at 11:02:52AM -0400, Axel Kohlmeyer wrote:
> 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. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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