[gmx-users] P-LINCS and nstlist
szilard.pall at cbr.su.se
Wed May 18 20:15:15 CEST 2011
> nstlist is more directly related to dt, and is often connected to the force
> field, as well. Values of 5-10 are standard. Setting nstlist = 1 is
> usually only necessary for EM, not MD. Excessive updating of the neighbor
> list can result in performance loss, I believe.
Not only can, but it surely will.
If you use nstlist=1 instead of say 10 which is a common value, you
essentially increase the neighbor search cost by a factor of 10. As
neighbor search contributes 6-8% to a typical PME runtime
(nstlist=10), that will be up to around 30-40% with nstlist=1.
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