Florian Dommert wrote:
* Mark Abraham <[email protected]> [2009-06-05 10:31:22 +1000]:
Borys Szefczyk wrote:
Dear GROMACS Users,
I would like to use the OPLS force field, but with additional scaling
factor for the Coulomb 1-5 interactions for certain atoms. More
precisely,
I want to use the standard 0.5 scaling for Coulomb and LJ 1-4
interactions
and 0.8 scaling factor for Coulomb 1-5 interactions. Is there a way to
do this within the topology file of Gromacs or do I need to modify
the code?
I can't think of a way to do this natively. Trying to use fudge-LJ
for 1-4 and pairs for 1-5 won't work (see 5.7.1 of manual).
Isn't the most naive way to define in the [ pairs ] section the further
requested 1-5 interactions ? However you will have to calculate the
epsilon and sigma of all the vdW-IAs, but this should not be a serious
issue.
The VDW may work, but not differently scaled 1-4 and 1-5 coulomb
interactions.
I had a molecule and gathered other charges. However as this new charge
distribution should not distrub the intramolecular energy landscape I
first defined all intramolecular nonbonded interactions within this
directive. This finally yielded exactly the same energy as the old force
field parameters.
Cheers,
Flo
Setting the number of exclusions for a moleculetype to 4, in a
forcefield with "generate_pairs = yes" and "fudgeLJ = 0.5" will
probably see pdb2gmx get everything except the 1-5 interactions
right. Then you post-process the .top from pdb2gmx in a (e.g.) perl
script, using the [ bonds ] entries to recognize 1-5 interactions
(which you add as [ pairs ]). You look up the normal LJ functions for
those atom types, then invoking the combination rule and your 0.8
scaling and write parameters on the [ pairs ] entry for each 1-5
pair. grompp will then blindly eat what you give it. Such 1-5
interactions will be reported by mdrun in with the normal LJ
interactions.
Mark
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
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
[email protected] [email protected] http://folding.bmc.uu.se
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