[gmx-users] cutt offs
ichorny at maxwell.compbio.ucsf.edu
Wed Jan 7 21:59:00 CET 2004
So what do I do when I have a solute that has a 1nm radius?
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
> different for the solute then the solvent. What cutt off distances is
> SPC parameterized for?
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).
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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
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