[gmx-users] bonded Buckingham interaction
frankie.montenegro at gmail.com
Fri Nov 9 10:47:02 CET 2007
Well, that's not an option, I am using a modified Morse interaction
was straightforward, I only needed to modify bondfree.c
But I saw in the manual (after sending the first email) the list of
files that need to be modified to add a bonded interaction, so I'll
try that. BTW, it would be much easier to use nonbonded Buckingham: is
there no way I could set up rvdw at 5A while keeping rcoulomb at 10A?
On Nov 9, 2007 4:14 AM, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Frankie Montenegro wrote:
> > Hi everyone,
> > I am trying to implement a force field for a metalorganic crystal. In this FF,
> > there is a Buckingham interaction between two neighboring atoms, O and Zn.
> > This interaction exists only for atoms on the same crystal site.
> How about using a Morse potential? It is quite similar.
> Alt. you can modify the Morse potential.
> > So, bonded Buckingham interaction added in [ pairs ] would be a
> > perfect solution.
> > But reading through the manual, it doesn't appear that bonded
> > Buckingham is supported
> > If this is the case (I'd love to be wrong here), what parts of code
> > would I have to modify
> > to make this happen (I hope this doesn't involve any major hacking)?
> > Thanks for your help.
> > F.
> > P.S. I should probably mention, I tried to use nonbonded Buckingham,
> > cutting it off beyond
> > a single crystal site, but this doesn't seem possible. My lattice
> > constant is about 12A,
> > Coulomb cuttof at 10A, and it seems like there is no suitable combination
> > of rcoulomb, rlist and rvdw that would cut off Buckingham short of
> > neighboring site
> > (while allowing Coulomb to reach that neighboring site).
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> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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