AMBER Archive (2003)

Subject: Re: the unit of velocity

From: David A. Case (case_at_scripps.edu)
Date: Wed Jan 08 2003 - 10:09:43 CST

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.

..dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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