[gmx-users] Scaled 1-5 interactions

Florian Dommert 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
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 interactions.
> Mark
> _______________________________________________
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Florian Dommert

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

Tel: +49 - 711 / 6856-3613
Fax: +49 - 711 / 6856-3658

EMail: dommert at icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: application/pgp-signature
Size: 194 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090605/c3e299a6/attachment.sig>

More information about the gromacs.org_gmx-users mailing list