Re: PME non-zero charge

From: Axel Kohlmeyer (
Date: Thu Nov 06 2008 - 16:49:09 CST

On Thu, 6 Nov 2008, Roman Petrenko wrote:

RP> Dear namd developers,
RP> how does namd handles PME calculations of systems with non-zero total charge?

not overly gracefully, but you cannot blame namd for that.
if you keep charged entities from crossing box boundaries,
it should be ok, but a neutral system is always better.

RP> and second related question: is there a routine for automatically
RP> adding counter-ions to proper places?

if you'd _read_ some of the e-mails posted to the list, you
would already know one of the possible answers. if you are particularly
interested in "proper", i recommend to have a look at the cionize
package (it is part of the VMD cvs, and thus should be at least in the
latest alpha versions).



Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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