[gmx-users] cutt offs
spoel at xray.bmc.uu.se
Wed Jan 7 21:57:01 CET 2004
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?
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
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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