VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu May 12 2011 - 14:00:30 CDT

Grant,
  I suspect it is likely that the PSF might be misformatted, and
that one of the values is going outside of the fixed-width fields.
Please send me a gzipped copy of the PSF file and I'll gladly have a look.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, May 12, 2011 at 02:56:44PM -0400, Axel Kohlmeyer wrote:
> On Thu, May 12, 2011 at 2:16 PM, Grant Schauer <grantschauer_at_gmail.com> wrote:
> > Hello all,
> >
> > I'm trying to solvate a small system consisting of a small peptide patched
> > to a novel residue built from CGenFF definitions.  When I attempt to
> > autoionize the system after solvating, I get a warning that I have a
> > non-integer charge.  In fact, it's measuring +67.08000009506941e.
> >
> > I get the same number with the following commands (regardless of whether
> > it's solvated):
> >
> > set sel [atomselect top all]
> > set charge [vecsum [$sel get charge]]
> >
> > But when I add up the charges from the PSF by hand, I get exactly the
> > integer (+2) that I expect, as specified in my topology file.  Autopsf runs
> > smoothly, with no complaints that I'm seeing.  I'm running VMD 1.9.
> >
> > Any suggestions? Thanks,
>
> VMD uses single precision floating point numbers,
> which have only about 7 valid digits in the mantissa.
> for a system with a large enough number of charged
> atoms, this kind of non-integer rest may be the consequence
> of simple rounding and truncation errors.
>
> axel.
>
>
> > Grant
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA. 

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