[gmx-developers] adding angle dependent non-bonded interactions?
jsu at caltech.edu
Thu May 6 23:56:17 CEST 2004
> -----Original Message-----
> From: gmx-developers-admin at gromacs.org
> [mailto:gmx-developers-admin at gromacs.org] On Behalf Of David
> Sent: Wednesday, May 05, 2004 1:29 AM
> To: gmx-developers at gromacs.org
> Subject: Re: [gmx-developers] adding angle dependent
> On Wed, 2004-05-05 at 02:33, Julius Su wrote:
> > Hello,
> > Is it possible/easy to add an angle dependent non-bonded
> > to GROMACS of the form --
> > E = (1 + (cos theta)^2) exp(-a r)
> > where theta is the angle between two vectors:
> > (1) radial vector.
> > (2) normal vector defined by atom and 2 bonded neighbors.
> > This would be used to implement a proton dynamics force field. I
> > already have the formulas for analytical gradients with
> respect to all
> > atoms involved.
> Possible, yes, easy, probably not. The difficult part is to
> get the three particles that are to interact. One could start
> with the simple neighboursearching algorithm and try to
> extend that. If you have fixed lists of atoms then it is
> quite simple on the other hand.
Hi David, could you tell me which files/functions do the following?
(1) non-bonded force computation.
(2) bond list: for each atom, access to the atoms bonded to it.
I assume the bond list doesn't change over time. Also, where are the
parameters for the GROMACS force field stored? Can one add new atom
types? New interaction types? Additional parameters? With this
information I could implement the potential in an easily user-modifiable
> > Thanks,
> > Julius
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> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics
> group, Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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