[gmx-users] cutt offs

[Ilya Chorny]

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.

Thanks

Ilya
   

-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
On Behalf Of David
Sent: Wednesday, January 07, 2004 12:11 PM
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] cutt offs

On Wed, 2004-01-07 at 21:58, Ilya Chorny wrote:
> So what do I do when I have a solute that has a 1nm radius?
> 
Is this still your single particle? In that case there is a problem,
otherwise each charge group in your molecule sees every water within the
cut-off... The twin range takes care of the long range forces. Don't
know about long range free energy contribution... 

> Ilya
> 
> 
> -----Original Message-----
> From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
> On Behalf Of David
> Sent: Wednesday, January 07, 2004 12:01 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] cutt offs
> 
> On Wed, 2004-01-07 at 21:45, Ilya Chorny wrote:
> > I ran a whole new set of calculations calculating the solvation of
> > molecules in SPC. I get significantly different results if I use a
> > cutoff distance of 1.4 for the LJ vs .8. I always assumed that the
LJ
> > interaction falls off much faster than that but I guess I was
ignoring
> > the Jacobian. Do other people see this kind of effect? The SPC water
> > becomes significantly more stable with the larger cutoff distances I
> > think this is where it would be useful to have a cutoff distance
that
> is
> > different for the solute then the solvent. What cutt off distances
is
> > SPC parameterized for?
> 0.9 nm.
> 
> However, the latest GROMOS proten force field is parameterized for
> twin/range 0.8/1.4 although most people probably run it with 0.9/1.4.
> (Oh, and nstlist should be 5 steps of 2 fs with shake).
> 
> > Thanks
> > 
> > Ilya
> > 
> > 
> > 
> > _______________________________________________
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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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