[gmx-users] Re: cut offs

[David van der Spoel]

On Thu, 2004-01-08 at 00:24, Ilya Chorny wrote:
> I looked at the code and Dispcorr seems to be a after the fact
> correction to the energy. It doesn't change the dynamics or in my case
> the resulting Coulomb structure.
No, because it is only an energy/pressure correction. It helps you to
get the correct energy and density. However, if you have structure
beyond the cut-off there is an error. You can check this by plotting an
RDF. Where it goes to one (or a bit beyond) you can in principle use a
cut-off for LJ.

> 
> Ilya
> 
> 
> -----Original Message-----
> From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
> On Behalf Of Ilya Chorny
> Sent: Wednesday, January 07, 2004 3:14
> To: gmx-users at gromacs.org
> Subject: RE: [gmx-users] Re: cut offs
> 
> 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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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