Hello,
To my knowledge the updates to the GIST code in AmberTools16/17 make it
compatible with the parallel version of CPPTRAJ, though I have not
personally ran the code parallel, would be worth a shot to try.
Another alternative is to break up the GIST region of interest into smaller
sub-regions and run GIST on the smaller regions in serial, we have a helper
script for this that we call biggergist and is summarized in the updated
tutorial in section 4f (bottom of page):
http://ambermd.org/tutorials/advanced/tutorial25/section4.htm. There is a
slight overhead for running the code to break up the regions and recombine
them at the end, but otherwise the biggergist approach scales linearly with
cpu's.
Hope this helps,
--Steve
On Mon, Aug 27, 2018 at 2:36 AM M RCC <mkr3j2c1.gmail.com> wrote:
> Dear Amber users,
> Running GIST calculations takes more time. Is there any way to speed up the
> calculation? and Is it possible to run parallel?
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Received on Tue Aug 28 2018 - 09:00:02 PDT
