[AMBER] pmemd.cuda - ewald error estimate?

From: Paul Brandt <brandt.j.gene.com>
Date: Tue, 1 Jun 2010 15:43:01 -0700



How do I enable the output of the "ewald error estimate" along with ntpr
info in amber11's pmemd.cuda


I am used to seeing it along with system info in the mdout files I get with
pmemd from the amber10 package, but I don't see it with amber11's


I am seeing a very big increase in performance by setting nfft(1-3) to 64.
My box size is ~160 angstroms, so I am wondering if I can get away with the
large grid size associated with using nfft=64. My benchmark runs are
finishing ~10% faster with nfft=64 vs. nfft=128, and setting these values
rather than letting pmemd set them gets me ~80-100% performance increase.


Any advice on assessing whether or not using nfft=64 or 128 values are
acceptable will be greatly appreciated.


Thanks very much!




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Received on Tue Jun 01 2010 - 16:00:03 PDT
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