[AMBER] 3D-RISM options

From: Ryan Pavlovicz <pavlovicz.7.osu.edu>
Date: Tue, 14 May 2019 14:45:27 -0700


I am interested using 3D-RISM for the purpose of predicting hydration sites
at protein/protein interfaces and would like some help/suggestions on how
to optimize both runtime and accuracy.

I understand that the use of treecode can help speed up the calculation. Is
the best way to implement this by setting --treeDCF 1 --treeTCF 1
--treeCoulumb 1? I see a bunch of other treecode-related flags and
suggestions in the Amber19 manual, but I don't quite understand which
should be used. Guidance here would be greatly appreciated.

I also understand that additional speed up can be accomplished by modifying
the grid spacing. For the rism3d.snglpnt calculations, would running with
--grdspc 0.5, 0.5, 0.5 --buffer 7 be reasonable for speedup for water
placement purposes without sacrificing too much accuracy? What are the
default values here?

Also, is there any known advantage to using SPCE vs TIP3P when it comes to
native water recovery? And how sensitive would the water placement be with
different NaCl concentrations? Is the 5 mM NaCl concentration used in Dan's
tutorial reasonable?

Finally, as far as output, I only need the O.dx file for placement of water
positions with placevent.py. Is there a way to silence the H1, Na+, and Cl-
output to prevent my disk space issues? Relatedly, is the calculation of
these required if I'm only interested in the O distributions?

Thanks in advance for your help!

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Received on Tue May 14 2019 - 15:00:02 PDT
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