[gmx-users] how to choose rlist and cutoffs

Robin C. Underwood rcunderw at purdue.edu
Thu Apr 1 18:56:19 CEST 2010


My system consists of large non-polar spheres in tip4p water, and the user
potential option is implemented to define vdw interactions. Because the radius
of the sphere is on the order of 1 nm, I am using a cutoff of 1.9 nm for the vdw
portion. I would like to save on computational expense by using a cutoff for
electrostatics (non-user defined) and choosing a much shorter electrostatics
cutoff, around 0.9 nm. Because I must also decrease my rlist value to 0.9, I am
wondering how this may effect the interaction energy between the sphere and
water. In particular, if my rlist is not much larger than the radius of the
sphere, or less than that radius, will I be neglecting important energetic
information with rlist=0.9 (even though the electrostatic interaction between
the sphere and water is practically 0)? 

I did see section 4.6.3 in the Gromacs manual, which leads me to think that it
is reasonable to decrease rlist because my vdw interactions should still be
computed, but I want to be sure this is correct.


Robin C. Underwood
Chemistry Department
560 Oval Drive
West Lafayette, IN 47907

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