[gmx-developers] pairs types for decoupling

David Mobley dmobley at gmail.com
Wed Apr 4 00:35:19 CEST 2007


I'm using the CVS version of 3.3.1 from last week, and am trying to
get the new pairs types Berk Hess has implemented to work for doing
decoupling. There's an old e-mail here on the subject, which is all
I've got to go by:

Berk wrote this:

>The idea is that for the solute to be decoupled one would replace
>the in its [ pairs ] section type 1 by type 2
>and exclude all intramolecular non-bonded interactions and replace
>add them again explicitly in a [ pairs ] section as type 3.
>BTW I tested it and it works.

Berk, any chance you can provide your test files so I can see how
exactly you're doing this?

I've been trying to do this for toluene, using Michael Shirts'
parameters which were published in supporting information; I've
previously reproduced his values without using decoupling so I know
they're correct. So far, I'm getting stuff that's ridiculously wrong
when I attempt decoupling, so I must be doing something wrong. Here's
what I'm doing:
1) I added bonds type 5 between all of the atoms that don't have
bonded interactions to ensure that the non-bonded interactions are
2) I changed all of the existing pairs to pairs type 2 (without
providing parameters, which I assume will mean they're still generated
according to teh combination rules for the A state)
3) Put all intramolecular nonbonded interactions into the pairs
section using pairs type 3 (again without providing parameters, since
they should be generated using combination rules for the A state).

What am I doing wrong? It would probably be very useful if one of us
put, either online or in the manual, a simple example topology that
demonstrates how to do this.


More information about the gromacs.org_gmx-developers mailing list