[gmx-users] pairs types for decoupling

Berk Hess gmx3 at hotmail.com
Wed Apr 4 09:56:32 CEST 2007

>From: "David Mobley" <dmobley at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "Discussion list for GROMACS development" <gmx-developers at gromacs.org>, 
>"Discussion list for GROMACS users" <gmx-users at gromacs.org>
>CC: Berk Hess <hessb at mpip-mainz.mpg.de>
>Subject: [gmx-users] pairs types for decoupling
>Date: Tue, 3 Apr 2007 15:35:19 -0700
>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:

This is not in 3.3.1, only in the development branch.

>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

It is easier to set nrexcl for your moleculetype higher,
or to add an [ exclusions ] section.

>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).

That is all correct.

>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.

The idea would be to let grompp do all the work.
But up to now this has not been implemented.


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