From: "David Mobley" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: "Discussion list for GROMACS development" <[EMAIL PROTECTED]>,
"Discussion list for GROMACS users" <[email protected]>
CC: Berk Hess <[EMAIL PROTECTED]>
Subject: [gmx-users] pairs types for decoupling
Date: Tue, 3 Apr 2007 15:35:19 -0700
All,
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:
http://www.gromacs.org/pipermail/gmx-developers/2006-March/001530.html
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
excluded.
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.
Berk.
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