On 19/05/2011 1:39 AM, Justin A. Lemkul wrote:
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.
Values of 10 with dt=0.002 are normal, but with longer time steps
smaller values of nstlist are wise. constant = nstlist * dt is probably
a wise rule of thumb.
Mark
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-- gmx-users mailing list [email protected]
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