[gmx-developers] adding angle dependent non-bonded interactions?
spoel at xray.bmc.uu.se
Wed May 5 10:29:21 CEST 2004
On Wed, 2004-05-05 at 02:33, Julius Su wrote:
> Is it possible/easy to add an angle dependent non-bonded interaction 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.
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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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