Thank you very much for such quick reply. I misunderstood the meaning of
"iteration" . I've confused the iteration of LINCS algorithm with molecular
simulation step.
Best wishes,
Slawek
Wiadomość napisana przez Justin A. Lemkul w dniu 2011-05-18, o godz. 17:39:
>
>
> 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-- gmx-users mailing list [email protected]
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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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