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.
-Justin
Thanks in advance,
Slawek--
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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