[gmx-users] pdb file ???

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Aug 21 10:20:57 CEST 2008

Hi Lin,

If you include bromide, you won't have excess charge... So, no need
for adding more counterions.



On Thu, Aug 21, 2008 at 8:20 AM, Chih-Ying Lin <chihying2008 at gmail.com> wrote:
> Hi
> It is the water-molecule system.
> For a molecule, like  R-N(CH3)3-Br,  I could make a pdb file  either
> include Br ion or exclude Br ion.
> If I exclude Br ion, I have to make Br ion as the counter ion for my system.
> If I include Br ion, I do NOT have to make Br ion as the counter ion
> since it will automatically become the counter ion.
> Am I right?
> Thank you
> Lin
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
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