From: John Stone (
Date: Fri Nov 15 2013 - 16:17:25 CST

Hi John,
  Sorry for the slow reply. I've been swamped finishing things before
I fly out to SC2013 early tomorrow morning. As you're discovering,
there are a number of challenges involved with the construction of very large
simulations. The tools we have built-into VMD work fine for "normal"
sized simulations, but for very large structures some of the GUI-based
tools don't perform as well as they could because they use old techniques
that worked fine when they were originally written, but that don't perform
well on huge structures with tens or hundreds of millions of atoms. The
other factor aside from the performance of the tools is that some of the
file formats (e.g. PDB and PSF) were never designed to be used for structures
in this size range, and the file formats can break in various ways, and/or
the file readers in various other programs may not like certain variants
of the file formats.

What we have done in VMD and NAMD to overcome these problems is
to make slightly non-standard variants of the PSF format that use
space-delimited fields, which are readable by NAMD, but not necessarily
by anything else. Another approach we have taken is to begin using
a experimental combined structure and trajectory format I named ".js"
(guess who) that should handle structures into the two-billion-atom
size range before problems start to crop up. This 'js' format can
be read and written by VMD and NAMD and psfgen, so that covers the
basics, although it won't help you if you're using other programs.

The area where things remain complicated even with just VMD/NAMD/psfgen
is that several of the VMD GUI-based structure building tools like
solvate, autoionize, etc predate any of these issues, and they haven't
been completely updated to do things the "new" way. For example, the
newest version of psfgen can do a pretty good job of generating a solvent
box without much help from the rest of VMD, but the current solvate
plugin doesn't yet take advantage of this feature of psfgen. So, at
the moment, several of the people in our lab that work on huge structures
end up writing their own custom scripts for some of the structure building
work rather than using the canned GUI-based plugins that you see in the
VMD extensions menu. We are working on updating the GUI-based structure
building tools in VMD for large systems, but since these issues only
affect a very small number of VMD users so far, we have chosen to
focus on developing the low level infrastructure and files formats
in VMD, NAMD, and psfgen, and leave the updates to the GUI plugins
until we're satisfied with how these things are working based on our
experiences with doing things the "new way".

To help you (and others) that may run into issues like this, I've asked
a couple of the people in our lab to share some of the scripts and suggestions
and this should help you get past some of these minor hurdles using VMD
to build your water box and subsequent steps. I'm CCing Jim Phillips who
works on NAMD+psfgen and Juan Perilla who has done several large simulations
and has written a bunch of his own scripts for some of these things.
We should be able to help you get your problem solved with a few

Once I get back from SC2013 late next week I should have more time to
answer remaining questions you may have.

  John Stone

On Mon, Nov 11, 2013 at 03:04:24PM +0000, John Grime wrote:
> Hello,
> I'm trying to create a large solvation box using VMD 1.9.2a33 for
> Linux/AMD64, and while the solvation script appears to work, VMD is unable
> to load the resultant PDB file.
> The "solvate.psf" file appears to be okay, but the "solvate.pdb" file
> produces the following error when read into VMD:
> Info) Using plugin pdb for coordinates from file /home/solvate.pdb
> ERROR) Incorrect number of atoms (10445941) in
> ERROR) coordinate file /home/solvate.pdb
> There should be around 50,000,000 atoms in the PDB file (this value is
> correctly reported when reading "solvate.psf").
> Can anyone help me to figure out what I can do, here?
> Also, the topology file which seems to accompany the solvate plugin has a
> somewhat different set of data for the TIP3 water compared to the contents
> of "toppar_water_ions.str" in the CHARMM36 force field set that I'd like
> to use. As the difference seems to only be the presence of "DONOR" entries
> in "toppar_water_ions.str" ("" in the solvate plugin only has an
> "ACCEPTOR" entry), I guess this difference is not significant as NAMD
> typically ignores thes H-bond entries?
> Thanks!
> J.

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349