[gmx-users] Scaled 1-5 interactions

[David van der Spoel]

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 
>>> 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
>> _______________________________________________
>> 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
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.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


-- 
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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++