[gmx-users] P-LINCS and nstlist
stachura.slawomir at gmail.com
Wed May 18 18:43:36 CEST 2011
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.
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.
>> Thanks in advance,
>> Slawek-- gmx-users mailing list gmx-users at gromacs.org
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> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
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> jalemkul[at]vt.edu | (540) 231-9080
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