AMBER Archive (2003)

Subject: Re: problem about virtual box?

From: Thomas Cheatham (cheatham_at_chpc.utah.edu)
Date: Thu May 01 2003 - 12:07:52 CDT

As Prof. Simmerling pointed out, you want to see if the molecule is
moving in the box. Your e-mails suggest, based on the first and
last frames that this is indeed the case. This is in fact highly
likely since:

> nscm = 0,

This implies you are not removing the center of mass motion (translation
in a periodic system). Due to initial velocity assignment there is a high
probability that there will be some initial motion (i.e. the sum of the
velocity vectors likely will not sum to zero). Further, if energy is not
rigorously conserved and you are coupling to a temperature bath, energy
drains will lead to a slow growth in COM translational (and rotational)
motion. Eventually all the temperature will be in translational motion.
You can check this by setting NSCM = 500 or some such and re-starting. If
the temperature drop is significant on the first step, you saw the flying
block of ice problem... For more info, see papers in JCC by Harvey
et al. (1998) and also by Chiu et al. (2000) and/or search for block of
ice on the archive.

When in a periodic system it is wise to set NSCM to be some finite value
(like 500 in a periodic gas phase system) to minimize this motional
artifact.

Good luck,

\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
| Departments of Medicinal Chemistry and of University of Utah
| Pharmaceutics and Pharmaceutical Chemistry 30 South 2000 East, Room 201
| & Center for High Performance Computing Salt Lake City, Utah 84112
|
| e-mail: tec3_at_utah.edu phone: (801) 587-9652 FAX: (801) 585-9119
\ http://www.chpc.utah.edu/~cheatham Offices: BPRP295A / INSCC 418