[gmx-users] Scaled 1-5 interactions
dommert at icp.uni-stuttgart.de
Fri Jun 5 22:39:25 CEST 2009
* Mark Abraham <Mark.Abraham at anu.edu.au> [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
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
> 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.
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Institute for Computational Physics
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EMail: dommert at icp.uni-stuttgart.de
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