On 10/5/12 5:35 AM, lloyd riggs wrote:
you have to play with the ratio usually of domain decompositions Vs. Grid size,
I had that error some time ago though, if you look at the generated .mdp from
the one you show (-o xxx.mdp), then look at the set FFT or xyz grid spacing and
play with it. It dosent like odd numbers or non-whole decompositions which are
based on the cpu's versus total size.
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
I might have remembered the answer wrong though, but someone will correct me if
I am wrong I hope.
Tweaking these settings may have a minor impact (and moreso on performance, I
would think). Decoupling an entire protein with explicit pair interactions and
exclusions is going to dominate DD cell size, as there are very long-range
interactions that are considered that normally are not. There is no really easy
way to get around a DD cell requirement upwards of 7 nm without changing
methodology entirely.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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