Hi,
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!
Thanks,
Olivia
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 06 2014 - 11:00:03 PDT
