* Mark Abraham <mark.abra...@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 issue. 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting!Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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