[gmx-users] Re: gmx-users Digest, Vol 53, Issue 140: uniform neutralizing plasma for PME (himanshu khandelia)

David van der Spoel spoel at xray.bmc.uu.se
Mon Sep 29 21:49:21 CEST 2008

Gerrit Groenhof wrote:
>> Type: text/plain; charset="iso-8859-1"
>> Is there an implementation in gromacs for using a uniform neutralizing
>> plasma with PME, to avoid use of counterions?
>> Thank you
>> -Himanshu
> Neutralization is done implicitly, by omitting out the zeroth plane 
> wavevector (m=0, see sec. 4.6 of the gmx manual). However, it is 
> advisable to use explicit ions always,  as the neutralizing background 
> charge leads to artefacts.

However, if you do, you should probably add ions to match the ionic 
strength in your solution. See e.g.
"Incorporating the effect of ionic strength in free energy calculations 
using explicit ions"
Author(s): Donnini S, Mark AE, Juffer AH, Villa A
Source: JOURNAL OF COMPUTATIONAL CHEMISTRY    Volume: 26    Issue: 2 
Pages: 115-122    Published: JAN 30 2005

> BEst,
> Gerrit
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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