Re: drude water in namd

From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Tue Jul 24 2012 - 16:22:57 CDT

The "Warning" line is self explanatory and intended.

The "ERROR" lines were an unintended consequence of some GB data structure initialization, but shouldn't have any adverse effect on the simulation beyond polluting the log file. I believe this problem to now be fixed, at least in the latest NAMD CVS source.

-Dave

On Jul 24, 2012, at 4:07 PM, Sandeep Patel wrote:

> Dear NAMD users,
>
> when attempting to run a script for drude water (216 water box, NVT, 298K) in namd, we obtain the following warning/error in the output, though the simulation does run to completion. before embarking on extensive validation ourselves, i would like to ask if others have observed this warning/error and what, if anything, has to be done to address it.
>
> Warning: CORRECTION OF ZERO MASS ATOMS TURNED OFF BECAUSE LONE PAIRS ARE USED
> ERROR
> ERROR
> ERROR
> ERROR
> ERROR
> ERROR
> ERROR
> ERROR
> .
> .
> .
> .
> .
>
>
> Thanks,
>
>

--
David J. Hardy, Ph.D.
Theoretical and Computational Biophysics
Beckman Institute, University of Illinois
dhardy_at_ks.uiuc.edu
http://www.ks.uiuc.edu/~dhardy/

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