[gmx-users] twin-range cut-offs and OPLS

[David van der Spoel]

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.
________________________________________________________________________
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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