AMBER Archive (2002)

Subject: Re: problem in restrt

From: Thomas Cheatham (cheatham_at_chpc.utah.edu)
Date: Fri Nov 22 2002 - 11:55:27 CST

> I had a problem with the restrt file, where I would get "****"
> for some of the coordinates. So I switched to writing unformatted
> restrt file (ntx=6, ntrx=0, ntx0=0)

The reason you are getting *****'s is of some concern; my guess is that
you are either

(1) using a solvated cap type system (i.e. blob of water) and that water
has drifted so far that it has blown the precision possible

or

(2) Using PME and haven't turned on the IWRAP=1 option leading to waters
effectively drifting to different periodic images (and eventually blowing
the precision).

The former can be "fixed" or inhibited by creating a large radius and weak
cap restraint to prevent these waters from drifting away.

> getting new box info from bottom of inpcrd
>

Since you are getting this message, it thinks the system is periodic,
hence perhaps you haven't turned on the IWRAP=1 option? This should fix
the problem.

I will have to investigate this issue with binary files further; as I
do not use the binary files, I do not have any experience. However, if
the box information is not present, it can be overridden in
the input file in the &ewald namelist by specification of a, b, c, alpha,
beta, gamma...

\ 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