AMBER Archive (2003)

Subject: Re: AMBER: Separation of a Water molecules

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Tue Nov 11 2003 - 22:13:41 CST

> We have encountered the very serious problem. It is
> that the water molecules in the middle of MD
> separates. The links and explanations of pictures
> wrote below.
>
> Is a countermeasure in this phenomenon?

Likely you are running a constant volume simulation and the density is not
correct leading to a "vacuum bubble" forming. You need to equilibrate
with constant pressure first to make sure the density is stable/correct
first.

If you were running constant pressure and see this problem, this is a more
serious issue...

\ 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
|
| tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\ BPRP295A / INSCC 418 http://www.chpc.utah.edu/~cheatham

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