Re: implementing angle dependent non-bonded interaction?

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon May 10 2004 - 14:51:26 CDT

Hello,

The source files of interest are ComputeNonbondedBase.h and
ComputeNonbondedBase2.h

Constants would probably be best placed in ComputeNonbondedUtil.C

The parameter reading code is Parameters.[Ch]

Hope that helps.
Brian

On Mon, 10 May 2004, Julius Su wrote:

> Hello,
>
> I'd like to add an angle dependent non-bonded interaction to NAMD of the
> form --
>
> E = (1 + (cos theta)^2) exp(-a r)
>
> where theta is the angle between two vectors:
> (1) vector joining atom1 and atom2
> (2) normal vector defined by the plane containing atom2 and its two
> bonded neighbors
> (e.g. water).
>
> Could someone point me to where the following files/functions are
> defined?
>
> 1. off-diagonal nonbond interactions (e.g. LJ)
> 2. bond list, for each atom access to the coords of atoms bonded to
> it.
> 3. parsing of parameter file; user defined parameters (e.g. force
> field file)
>
> This potential would allow us to implement a proton dynamics force field
> our group is developing.
>
> Thanks,
>
> Julius
>

*****************************************************************
**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) 424-6605 **
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