[AMBER] Questions for pH-REMD by Jason Swails

From: M Olivia Kim <olivijuly.gmail.com>
Date: Wed, 6 Aug 2014 10:43:35 -0700


I have been using the pH-REMD by Jason Swails, implemented in the Amber 14 release and have a couple questions:

1) I ran the pH-REMD for the pH range between 2 to 7.5, and want to add new replicas at pH 1, 1.5, 8, and 8.5. In that case, should I rerun the entire production run involving the new, extended pH ladder (pH 1-8.5)? Or can I restart the production run by adding the new replicas to the restart files from the old pH-REMD of pH 2-7.5?

2) Jason Swails mentioned in his wiki that he implemented the pH-REMD on GPU. However, when I try to run the pH-REMD on GPU like:

pmemd.cuda -ng 12 -groupfile groupfile

it crashes with an error message saying that -ng is not a valid option for pmemd.cuda. It basically requires the usual command like -O -i Does anyone have idea how to make it run on GPU?

Thank you in advance!

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Received on Wed Aug 06 2014 - 11:00:03 PDT
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