FW: [gmx-users] tabulated potential both on pairs and non-bonded interactions / different cutoffs

Berk Hess gmx3 at hotmail.com
Fri Jul 4 10:47:33 CEST 2008

From: gmx3 at hotmail.com
To: lastexile7gr at yahoo.de
Subject: RE: [gmx-users] tabulated potential both on pairs and non-bonded	interactions / different cutoffs
Date: Fri, 4 Jul 2008 10:14:14 +0200


It is completely clear to me if your 1-4 and 1-5 interactions use the same potential types and cut-off's.
If they do, you can do it with the user tables.
Set nrexcl in the topology to 4.
I think you will then have add the 1-5 interactions manually to the [ pairs ] section.
mdrun has separate input files for non-bonded and bonded interactions.
You will have to fill these tables with the functions with the right cut-offs and
switching functions.


Date: Tue, 1 Jul 2008 14:48:21 +0000
From: lastexile7gr at yahoo.de
To: gmx-users at gromacs.org
Subject: [gmx-users] tabulated potential both on pairs and non-bonded	interactions / different cutoffs


trying to implement my force field into gromacs I have figured out that it is of vital importance to use diferrent cut-offs among different kind of atoms. 

I have 1-4 and 1-5 interactions with a set of epsilon and sigma parameters and the non bonded interactions (more than 4 bonds appart) with a different set. Every interaction among different type of atoms have different rvdw-switch and rvdw cutoffs.

As a result I have to use a tabulated potential both for 1-4 and 1-5 interactions AND non-bonded interactions (1-6 and above). My question is how is it possible someone to do that in gromacs. How gromacs would be able to discern whether the interaction is 3 or 4 bonds appart OR more than 4 bonds?

In case I cannot use tabulated potential for the interactions I'm
interested in, could I keep the pair interactions as they are up to now
under the pairs section and use at least tabulated potential for the
non-bonded interactions?

In any case of the above what would be the meaning of rvdw-switch and rvdw cutoffs in the mdp file?

The number of different interactions I have are 6. Is it possible while tabulating the non-bonded interactions to have both energy and pressure correction? 

I have also seen that I can use reduced parameters (eplsilon and sigma) for all the non-bonded interactions, yet (correct me if I'm wrong) I do not think that this solves the problem of different cutoffs. That way only one interaction would have the correct cutoff.

Unfortunately all my efforts up to now with one global cutoff don't bring the anticipated results.

Thank you in advance,

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