Re: simulations space partitioning parameters

From: Josh Vermaas (
Date: Wed Jul 14 2021 - 08:52:17 CDT

Hi Nancy,

The parameters are force field dependent, and impact performance as well
as accuracy. Larger cutoffs generally improve accuracy, but cost more
non-bonded evaluations per timestep which lowers performance. CHARMM
force fields are parameterized with 10, 12, and some number greater than
12 (usually I use 14) for the switchdistance, cutoff, and pairlist
distance. AMBER, depending on the biopolymer, is something like 7 or 8,
10, 12. I'm less familiar with the numbers other force fields recommend,
but the infamous reviewer #2 will (should?) complain if you don't follow
the strictures dictated by the force field you pick.


On 7/14/21 7:45 AM, Nancy Singh wrote:
> Hii,
> I am a little confused about the space partitioning parameters
> switchdist, cutoff and pairlistdist.
> I have read the manual and know that cutoff indicates the distance
> beyond which electrostatic and Van der waals interactions are cutoff.
> I want to know if there are any particular criteria for selecting
> values for these parameters? and also if these parameters can
> affect our simulations or how the protein residues are interacting
> during simulations?
> Thank you
> Regards,
> Nancy

Josh Vermaas
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University;!!DZ3fjg!pbRK3c9EtT20A9z7imo1EFKu_J7luEqxBFFlDF7yV6AVWegxQ6NNHWXApXnwBnETjQ$ 

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