[gmx-users] Re: cut offs

Ilya Chorny ichorny at maxwell.compbio.ucsf.edu
Thu Jan 8 00:15:01 CET 2004


I looked in the manual but it doesn't give much detail about this
correction. What exactly does Dispcorr do? Also I have never run MD code

with abrupt cutoffs. Is that what you guys do and how does it affect
your results? 



-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
On Behalf Of Michael Shirts
Sent: Wednesday, January 07, 2004 2:17 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] Re: cut offs

Adding a dispersion correction corrects for the truncation of the r^-6
term in
the LJ term in a "mean field" way.  Read over the manual for more
It's the DispCorr keyword in an .mdp file.  This should make the
density/energy of a box of water almost independent of the VdW cutoff
chosen, as long as it's over 0.8 nm or so.

Right now, the dispersion correction is only calculated correctly for
cutoffs.  I have given code to Erik Lindahl to calculate the dispersion
correction correctly for Shifted and Switched VdW cutoffs as well --
presumably that will be in later versions of Gromacs.


> I currently have both cutoffs LJ and Couloumb cutoffs set 1.5 nm. The
> of the water in 10% more stable and more dense with a 1.5 nm LJ cutoff
> a .8 nm LJ cutoff. This causes the solvation free energies to increase
> dramatically about 50 % in some cases. Any advice on how to hack
gromacs So
> that I can have a different cuttoffs for the solute-h2o than h20-h20.


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