[gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

Lee Soin nomadoro at gmail.com
Mon Jul 27 15:56:08 CEST 2009

I see in the .top file generated by pdb2gmx:
[ pairs ]
;  ai    aj funct            c0            c1            c2            c3

The [ pairs ] directive accepts these four parameters c0, c1, c2 and c3. Do
c2 and c3 parametrize electrostatic interactions? And what do they stand for
respectively? Thanks!

2009/7/27 Mark Abraham <Mark.Abraham at anu.edu.au>

> Lee Soin wrote:
>> My problem is actually as follows:
> Please describe in as full detail as reasonable the first time :-)
>  I have three groups of atoms: A, B and C. Now I want to keep full
>> interaction between A-B and A-C, but only retain the repulsive part of VDW
>> interaction between B-C. I'm using the OPLS force field. It seems to me
>> that
>> the parameters for OPLS in the .itp files are specified for each atom, so
>> is
>> there any way to treat the interaction pairwise?
> Yes, use [ pairs ] directives to overrride the atomtype-based lookup. That
> will be tedious if there are many such atoms. Read parts of chapter 5.
> Probably, no force field was parameterized to reproduce whatever it is
> you're trying to observe.
> Mark
> _______________________________________________
> 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

Department of Physics
Nanjing University, China
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090727/a579dfe1/attachment.html>

More information about the gromacs.org_gmx-users mailing list