AMBER Archive (2002)

Subject: Re: Sander: check COM velocity, temp: 0.000000 0.00(Removed)

From: Thomas Cheatham (cheatham_at_chpc.utah.edu)
Date: Fri Nov 08 2002 - 23:49:21 CST

> I'm running a molecular dynamic simulation, and in the output file, I have
> found repeatedly one "suspicious" message.
>
> check COM velocity, temp: 0.000000 0.00(Removed)

This message is stating the center of mass translation is being removed
and that the amount of velocity and effective temperature that is in COM
translation is 0.000000 and 0.00, respectively. In your case these
numbers are zero so no COM translation has built up and therefore
effectively no motion is removed.

[If thing's are running reasonably well, i.e. energy is conserved, very
little energy should drain into translational motion. The only time you
should see significant numbers in the above message is after initial
random velocity assignment (which will likely lead to a small
translational componenet) of if energy is poorly conserved (due to
infrequent pairlist update, no buffered/skin pairlist, SHAKE tolerances
that are too low, time steps that are too large, ...). If large numbers
are seen, this is a problem].

Perhaps we should change the message to simply say:

"COM motion removed: translational velocity and temp were 0.000000 and 0.00"

Sorry for the confusion.

\ 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