Re: AMBER: NaCl ion pairs in TIP3P water box

From: Nathan A. Baker <>
Date: Wed, 24 Sep 2003 20:14:47 -0500

Thanks to all who replied; it appears this phenomenon may not be as
surprising as I thought. I've lumped the replies below as a summary
and included a few more comments. However, I do have a general
question: has anyone tried to calculate solubility products for salts
in TIP3P?

David A. Case <> (09-24-2003 14:09:06-0700):
>Nathan: I hope Tom Cheatham or Tom Darden will speak up here, but I suspect
>that this is a force-field "problem". Do the ion pairs break up if you
>soldier ahead and go to 300K, or do they remain? I don't have any explicit
>relevant experience, but I seem to have heard of similar problems through
>the grapevine. (If you haven't done so, ask Jay what he thinks...)

In fact, I started running the salt/water box becuase of a disaster
with a protein system at 800 mM NaCl. For the protein system, not
only did the ion pairs persist at 300 K but, after 500-1000 ps, they
nucleated larger "crystals" of salt. Some of these crystals contained
as many as 8 ions! Not surprisingly, this wreaked havoc with my free
energy calculation...

I haven't carried the salt/water box out much longer at 300 K; once I
started spotting 3-4 pairs again, I figured I was in trouble...
However, now that I know I'm not encountering anything too unexpected,
I'll pursue this trajectory a bit further.

I have definitely been talking with Jay about using AMOEBA on the same
system; hopefully polarizability could make the difference here.

Jiri Sponer <> (09-24-2003 23:41:27+0200):
>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.

That definitely seems likely; I'm planning to talk with Jay Ponder
about using his force field for this system.

>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.

Very interesting idea; I'll have to play around with the charges a

Bill Ross <> (09-24-2003 13:53:39-0700):
>> However, I invariably end up with ion pairs by the time I reach the
>> 150-200 K stage of this procedure.
>That's the norm. Same-charge ions form pairs with pairs of
>waters, e.g.
> H H
> O
> + +
> O
> H H
>Bill Ross

Interesting -- I do see some ion pairs like this but the majority are
NaCl pairs.

Ioana Cozmuta <> (09-24-2003 15:30:26-0700):
>I did some simulations with KCl at 1M and SPC/M water for about 1ns. I've
>started with two different configurations: the first in which ions are
>randomly placed in the unit cell. The second in which I study crystal
>dissolution. I end up with approximately same average behaviour thus I
>think that at high concentration pairing and even clustering of ions is
>not impossible and that's what some experimental chemist think as well.
>It's a dynamic equilibrium however, not all the time the same ions

Yes; this does seem possible. However, I'm worried that the lifetime
of these pairs (and larger clusters) will be much longer than I can
simulate. Was 1 ns sufficient to observe the dissolution of the
crystal you were examining?

M. L. Dodson <bdodson.scms.utmb.EDU> (09-24-2003 18:53:22-0500):
>This seems like a problem that should be solvable by ab initio
>methods, maybe?
>Bud Dodson

Or polarizable force fields! :)

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
PGP key:
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Received on Thu Sep 25 2003 - 02:53:01 PDT
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