AMBER Archive (2003)

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

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Sun Aug 17 2003 - 22:08:00 CDT

Hi,

Does the diffusion module under ptraj automatically unfold any type of
trajectory. I am particularly interested in .dcd trajectories generated in
NAMD.

Thank you,
Ioana

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On Tue, 12 Aug 2003, Thomas E. Cheatham, III wrote:

>
> > 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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