[gmx-users] Scaled 1-5 interactions
David van der Spoel
spoel at xray.bmc.uu.se
Sat Jun 6 08:06:26 CEST 2009
Florian Dommert wrote:
> * 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
>>> I want to use the standard 0.5 scaling for Coulomb and LJ 1-4
>>> 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
The VDW may work, but not differently scaled 1-4 and 1-5 coulomb
> 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.
>> 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
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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
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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