AMBER Archive (2003)

Subject: Re: AMBER: NaCl ion pairs in TIP3P water box

From: David A. Case (case_at_scripps.edu)
Date: Wed Sep 24 2003 - 16:09:06 CDT


On Wed, Sep 24, 2003, Nathan A. Baker wrote:
>
> 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.
>

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...)

..regards...dave

-- 

================================================================== David A. Case | e-mail: case_at_scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | http://www.scripps.edu/case ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu