From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Mar 25 2011 - 04:52:09 CDT
Dear all,
Is there any advisable limit on how many quadrants a 2D torsional free
energy scan using ABF can be divided? Scaling the simulation by splitting
the ABF calculation has the advantage that each part runs independently, so
there are no scaling issues.
On the other hand one is wary of introducing artifacts by the artificial
wall constraints (as in figure 6b in [1]).
I'm asking because over the weekend I will have access to 512 cores. My
simulation has 16.000 atoms, so just throwing more cores at it will not be
very effective. (I will of course run the necessary scaling benchmarks
before I start)
Currently I'm spliting the ABF calculation into 8 parts. Would 36 parts be
too much? This would then be pieces of 6x6 points.(The bin width is 10
degrees and the range form -180 to 180).
I know this strongly depends on the system, but I'm asking for the "gut"
feeling:)
Thank you & best regards,
Ajasja Ljubetič,
Young reasercher,
Laboratory of biophysics,
Institute Jožef Štefan,
Ljubljana, Slovenia
1. Christophe Chipot and Jérome Hénin, “Exploring the free-energy
landscape of a short peptide using an average force,” The Journal of
Chemical Physics 123, no. 24 (2005): 244906.
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