[AMBER] curiosity about sander reading a traj being written by GPU code

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Fri, 5 Feb 2021 22:09:10 +0530

Dear All,
Do the Amber MD codes lock the files that are in use or being written?
I'm running MD (pmemd.cuda) on GPU, then estimating SP energies with sander
on CPU.
Now since sander on CPU is slower than the GPU MD code (is it true for SP
sander vs MD on GPU? I think it is slower but not by a very large margin).
Is it possible to read an MD trajectory using sander (with -y option) to
estimate SP Es, while it is being written by the GPU code?
If this is possible, then what are the chances that sander will catch up
with the GPU code while reading trajectories that GPU code writes.

Although this is not absolutely necessary, it might just save a few hours
of time, since one wouldn't have to wait for the GPU MD to finish before
starting the sander SP calculations.
Looking forward to valuable insights and suggestions from the list.
thank you and best regards.

Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
Assistant Professor,
Department of Pharmacy,
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
ORCID ID: https://orcid.org/0000-0003-4015-2941
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Received on Fri Feb 05 2021 - 09:00:02 PST
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