Hello all,
I was wondering if amber20 is able to periodically dump intermediate
frames/traj/energies to a PDB file during an MD run. The question has to do
with getting snapshots of partial results as the process runs.
I know this is possible with CHARMD and NANMD (under Discovery Studio).
Partial frames are stored and updated periodically at the UI and the user
gets to see changes every few seconds.
Rosetta also ships a Pymol plugin (by Baugh, etc al) that updates a remote
pymol UI session during MD runs, so you can visually see what's going on as
computations occur.
If not yet available, writing a few lines to dump trajectory/energy/frame
data wouldn't take much effort. I'm sort of new to the amber code, so I
wouldn't have a clue on where to embed a probe during a running MD (I'm
guessing the pmemd/sander source?). I would gladly do so.
Thanks in advance for any hints.
Pedro
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Received on Mon Nov 29 2021 - 03:00:03 PST
