[AMBER] GaMD problems with different computers.

From: Seibold, Steve Allan <stevesei.ku.edu>
Date: Thu, 12 Dec 2019 19:12:25 +0000

Hi all

I started a run (GaMD pmemd.cuda) on a GPU system which ran fine for 2ns. I then followed this using "all" the same input files on a CPU system (GaMD pmemd.MPI) and again, it ran fine for 2ns. However, I switched to another cluster system and attempted to run on their pmemd.MPI and I got "vlimit exceeded....Coordinate resetting cannot be accomplished, deviation is too large" within in the first step or so. So, the protein setup is stable on GPU and a separate CPU system, but not on a different Cluster CPU. Can someone inform me as to the problem?

I also tried "starting" GaMD on the cluster CPUs with the system that had been running for 2 ns on GPUs, but it still failed with error "Coordinate resetting (shake) was not accomplished "...

Thanks, Steve
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Received on Thu Dec 12 2019 - 11:30:02 PST
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