[gmx-users] Re: cut offs

[Ilya Chorny]

Michael,

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? 

Thanks

Ilya


-----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
details.
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
distance
chosen, as long as it's over 0.8 nm or so.

Right now, the dispersion correction is only calculated correctly for
abrupt
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.

Cheers,
Michael


> I currently have both cutoffs LJ and Couloumb cutoffs set 1.5 nm. The
energy
> of the water in 10% more stable and more dense with a 1.5 nm LJ cutoff
then
> 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.

Cheers,
Michael

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