VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu May 12 2011 - 13:56:44 CDT

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.