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

Marco Möller moeller at mail.uni-mainz.de
Thu Mar 17 10:34:22 CET 2005

Dear All+ACE-

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               +AD0-  0.8
coulombtype         +AD0-  cut-off
rcoulomb            +AD0-  1.4
rvdw                +AD0-  0.8
constraints         +AD0-  all-bonds
integrator          +AD0-  md
dt                  +AD0-  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.

Thank You very much+ACE-
Marco Moeller

Marco Moeller
Inst. f. Molekulare Biophysik
Johannes Gutenberg - Universitaet
55118 Mainz, Germany

moeller AT uni-mainz DOT de 

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