Re: amber-developers: cap, igb=10 (or not) and charge perturbation

From: Ray Luo <>
Date: Sat, 4 Mar 2006 18:13:10 -0700

Hi Lachele,

>Someone here is trying to do a charge perturbation in Amber9.
>He is successful when he uses a cap with igb=10, but not
>otherwise (with other variables controlled: same two top
>files, etc.).
That's interesting ... igb=10 has not been tested with TI simulations,
though this has been a goal.

>It doesn't look like an input issue because when it isn't
>successful, the job goes for a few thousand steps and seems to
>just hang (using cpu according to top, but not writing any
>output for, like, 20 hours). If it were an input issue, it
>probably wouldn't go at all. Feel free to disagree, of course.
I'm not sure about cap without igb=10 for TI simulations ...


Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail:
Home page:
Received on Wed Apr 05 2006 - 23:49:41 PDT
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