[gmx-users] twin-range cut-offs and OPLS
David van der Spoel
spoel at xray.bmc.uu.se
Thu Mar 17 11:09:27 CET 2005
On Thu, 2005-03-17 at 10:34 +0100, Marco Möller wrote:
> Dear All!
> I learned from the Gromacs User Guide and from some web tutorials about
> MD how to use twin-range cut-offs for faster calculation of the
> non-bonded interactions. The examples were given for the GMX force
> field. As my aim is to do some first MD-runs on small peptides (13-23
> aminoacids) to learn and catch up with the method of MD without wasting
> to much computer time by using mindless parameters in the mdp files: I
> appreciate any comments on the topic of choosing sensefull parameters to
> bring a newbie on its MD way.
> My current parameters used with GMX-FF are
> in a box whith a distance of 1.0 nm between box-edges and nearest
> peptide atom:
> rlist = 0.8
> coulombtype = cut-off
> rcoulomb = 1.4
> rvdw = 0.8
> constraints = all-bonds
> integrator = md
> dt = 0.002
> If I want to use the Gromos96/SPC and particularly the OPLSAA/TIP5P
> force-fields, can I just copy this parameters, or do I have to consider
> some different boundary values? I read that it would be best to choose
> the parameters in the range of values the force-fields were optimized
> for, but up to now I did not found the information about which are the
> perfect parameters with each of the Force-fields and nothing about
> adopting them to the twin-range procedure.
For production we use something like:
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.4
nstlist = 5
constraints = all-bonds
integrator = md
dt = 0.002
If you choose not to use PME you want to change rcoulomb to 1.4 as well.
> Thank You very much!
> Marco Moeller
> Marco Moeller
> Inst. f. Molekulare Biophysik
> Johannes Gutenberg - Universitaet
> 55118 Mainz, Germany
> moeller AT uni-mainz DOT de
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David van der Spoel, PhD, Assoc. 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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