[AMBER] tMD and pmemd

From: Francesco Gentile <fgentile.ualberta.ca>
Date: Wed, 29 Apr 2020 17:00:17 -0700

Hello everyone,

I would like to perform targeted MD simulations on GPU with pmemd (Amber
16). I understand tMD has not yet been implemented with pmemd but I was
thinking about modifying a bit the source code to include that feature. For
example, by using something similar to what was done in the sander
code. Could you let me know if this sounds reasonnable to you and if there
is way to do that while keeping reasonnable performance on GPU? I guess tMD
was not implemented because of RMSD calculation which may be not convenient
for GPU architecture right?.... Do you have any advice?

Thanks a lot,

Francesco Gentile, Ph.D.
Vancouver Prostate Centre, Vancouver BC, Canada
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Received on Wed Apr 29 2020 - 17:30:01 PDT
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