From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Nov 05 2003 - 15:22:16 CST
You can get the source from the main namd webpage....
Not sure about the notes. The source code for namd does not contain an
abundance of comments. a few emails to Jim though should get you through
if can program in c++...
Brian
On Wed, 5 Nov 2003, AMIT PALIWAL wrote:
> Hi All,
> Sometime back i had written about doing MD with a hard sphere and the
suggestion was to implement it as a r-12 potential as given below.
Can anyone help me out as to how one can 'actually' implement this
spherical harmonic boundary conditions code? where are these source
file and are there any notes available?
> thanks,
> Amit.
>
>
> I'd suggest modeling it as a very stiff "soft" interaction.
> > >
> > > If you want a single sphere, substantially larger than an atom and
> > > locatedat a fixed location then you can probably adapt the
> > > spherical harmonic
> > > boundary conditions code (src/ComputeSphericalBC.[Ch]) to implement
> > > whatever hard-core potential (like (r-r_0)^(-12)) you want.
> > >
> > > Otherwise, you'll need to be a little more specific in what you want.
> > >
> > > -Jim
>
-- ***************************************************************** **Brian Bennion, Ph.D. ** **Computational and Systems Biology Division ** **Biology and Biotechnology Research Program ** **Lawrence Livermore National Laboratory ** **P.O. Box 808, L-448 bennion1_at_llnl.gov ** **7000 East Avenue phone: (925) 422-5722 ** **Livermore, CA 94550 fax: (925) 422-6605 ** *****************************************************************
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