AMBER Archive (2003)

Subject: Re: AMBER: question to calculate diffusion coefficient under periodic boundary conditions.

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Tue Aug 12 2003 - 14:32:36 CDT

> I was wondering if anyone is willing to share how to get the diffusion
> coefficient of particles when the periodic boundary conditions are
> included.

Following up on what David Case just mentioned, it is also possible to
unwrap a periodically imaged trajectory (if the time between frames is
short enough to not allow large scale translation of a molecule, i.e. >
1/2 box size between frames). In other words, if the simulation was run
with IWRAP=1, code can detect that a particle was imaged and unimage it
for the diffusion analysis. This is currently done in ptraj (ONLY for
orthorhombic i.e. 90x90x90 unit cells) within the diffusion command. To
make this more general, ptraj would have to modified to create an unimage
command or the diffusion command modified to allow for general triclinic
unit cells.

\ 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

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