VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Nov 11 2013 - 15:55:34 CST

Hi John,

I tried recreating the problem by making a 100nm watercube (98M atoms),
and it does work for me. 10M is kind of a weird place for VMD to get
stuck, as its not on the boundary of anything that might cause VMD to
baulk (for instance, at around 1M atoms, pdbs made by psfgen stop
reporting atomic serial numbers). Have you looked at the file in a text
editor to see if there is anything strange going on near that line? If
that looks alright, perhaps your machine ran out of RAM when loading the
pdb? My test system was around ~20GB all told, and while loading into
VMD took up around 24GB of RAM. Something else you could try is to use
the js file format. These are compressed, so they load faster, and have
both topology and coordinate information stored in a single file. The
folks in lab that need multimillion atom simulations use these almost
exclusivly. To make one, you need to specify that you are outputting to
a js file:

solvate -o solvate.js -minmax [list [list 0 0 0] [list 1000 1000 1000]]

Note that your psfgen build needs to support plugin I/O for this to work
(mine doesn't. :(). Perhaps someone with more experience working with
massive systems might chime in on this point.

In terms of the donor/acceptor entries, those have not been used for
dynamics since v. 19 of the CHARMM force field, although for the
purposes of analysis, there is a par_hbond.inp file still in the
distributed parameter set, which warns you explicitly against using them
for dynamics. Thus, the differences between the topology for
toppar_water_ions and wat.top are almost purely cosmetic, as both depend
on the same TIP3 water model.

-Josh

On 11/11/2013 09:04 AM, 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" ("wat.top" 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.