Re: AMBER: NaCl ion pairs in TIP3P water box

From: Jiri Sponer <>
Date: Wed, 24 Sep 2003 23:41:27 +0200 (MEST)

Dear Nathan,

I think this could be due to atom-atom pair-additivity.
There is no polarization and CT towards the (and through)
the ion first coordination shell and actually I can imagine
this type of a dysbalance as one of the possible outcomes.
Point charge is another approximation that causes troubles
with ions, especially anions.

I would possibly try to reduce the charges below 1 in
absolute value to see if any change due to a shift in compensation
of errors.

Best wishes, Jiri

Jiri Sponer
Professor of Biophysics
Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
fax: 420 5412 12179
phone: 420 5415 17133

> However, I invariably end up with ion pairs by the time I reach the
> 150-200 K stage of this procedure. The appearance of ion pairs does
> occurs with or without Step 4; I added that as an additional attempt
> to keep the ions apart.
> Does anyone have an idea what I might be doing wrong here?
> Thanks,
> Nathan
> --
> Nathan A. Baker, Assistant Professor
> Washington University in St. Louis School of Medicine
> Dept. of Biochemistry and Molecular Biophysics
> Center for Computational Biology
> 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110
> Phone: (314) 362-2040, Fax: (314) 362-0234
> URL:
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Received on Wed Sep 24 2003 - 22:53:01 PDT
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