Re: AMBER: Separation of a Water molecules

From: Thomas E. Cheatham, III <>
Date: Wed, 12 Nov 2003 21:16:38 -0700

> Since our customer's permission is required,
> it is very difficult to offer raw input file.

Professor Simmerling was referring to the "mdin" file NOT the set of
coordinates and parameters. The "mdin" file is very unlikely to be a
company proprietary secret. In principle, the actual system under study
(coordinates/parameters) could be...

The mdin file will show if indeed you *are* runing constant pressure and
if you are using a reasonable coupling constant. Additionally, it will
highlight other potential issues (related to belly or position restraints)
or other anomolies.

Good luck with tracking your problem.

\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy, Depts of
| Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry
| Adjunct Asst Prof of Bioengineering; Center for High Performance Computing
| University of Utah, 30 South 2000 East, Skaggs 201, Salt Lake City, UT 84112
| (801) 587-9652; FAX: (801) 585-9119
\ BPRP295A / INSCC 418

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Received on Thu Nov 13 2003 - 04:53:01 PST
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