Re: [AMBER] fix the positions of EP

From: case <case.biomaps.rutgers.edu>
Date: Fri, 8 Oct 2010 11:24:47 -0400

On Fri, Oct 08, 2010, William Flak wrote:
>
> If you don't mind, why you fix the position of EP in the local frames as
> written in extra_pts.f
> !+ fix the positions of EP in the local frame/coord depending
> !+ on the kind of frame and atom types.

"fix" here means "compute"

> We use parameters for the EP. don't we?

No. The distance of the EP's from the real atoms is determined by the "bond
length" parameter, and I think angles are determined by "bond angles". But
the ways in which the positions of the EP's are determined from the real
atoms, and the forces on the EP's are transferred back to the real
atoms, is hard-wired in the code.

....dac


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Received on Fri Oct 08 2010 - 08:30:03 PDT
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