Re: [AMBER] Question about Extra Point

From: David A Case <>
Date: Fri, 22 May 2015 07:47:16 -0400

On Fri, May 22, 2015, zhouhaibin2008.ok wrote:

> Recently, I calculated the solvation energy of an organic molecule
> with chlorine atoms included. Better strategy is to add virtual
> sites(massless) to chlorine atoms. These virtual sites are pure
> charge sites with no Lennard-Jones interaction. I wonder if it is
> feasible to perform molecular dynamics with this virtual sites by
> the PMEMD engine or there are some tutorials I can refer.

pmemd and sander support a limited set of "extra points", but these are really
only documented in the code itself. See the define_frames() routine in
extra_pts.F90 in sander. You can see if what you want fits one of the
existing models, or add new types of extra points by modifying the code. There
is no user interface for defining new frames (i.e. new types of extra points.)


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Received on Fri May 22 2015 - 05:00:02 PDT
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