Re: the unit of velocity

From: David A. Case <>
Date: Wed 8 Jan 2003 08:09:43 -0800

On Tue, Jan 07, 2003, Jian Zhang wrote:
> In the output file of Sander, does the Etot include
> the energy of waters (I add some thousands of waters
> around the protein)? If so, how can I get the totaly
> energy of protein only, must I write programs to
> analysis the topology and trajectory files of sander
> myself?

See the mm/pbsa section of the manual.

> And What's the unit of velocity in mdvel file?

See the FAQ on "units" at the Amber web site.
> some FAQ questions, sorry.

We *do* encourage people to look at the FAQ before posting questions here.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Wed Jan 08 2003 - 08:09:43 PST
Custom Search