[gmx-users] P-LINCS and nstlist
Justin A. Lemkul
jalemkul at vt.edu
Wed May 18 17:39:57 CEST 2011
Sławomir Stachura wrote:
> Dear Users,
> I am not sure if I understood properly how P-LINCS should parametrized for simulation. In manual it's written that "one coordinate communication step is required for the initial LINCS step and one for each iteration"; so as coordinate communication is tightly binded to neighbor searching, does it mean that nstlist should equal "1"? I mean - should neighbor list be updated every simulation step for proper use of constraints in parallel with LINCS?
> I have searched for the answers in mailing list, but I was unsuccesful in finding tone.
The quoted passage is related to domain decomposition communication, not
neighbor searching. The algorithms involved are rather complex, and (usually)
work without much manual intervention.
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.
> Thanks in advance,
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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