Dear AMBER developers,
We are working on an idea to reweight the true kinetics from metadynamics
simulations, and we have a couple of questions regarding running
metadynamics on AMBER:
1. Are the forces that are written in the output (ntwf=-1) the biased
forces with the potential from metadynamics or just the forces that are
estimated from the potential gradient? This would be critical for us to
decide whether we need to account for metadynamics forces externally.
2. Since the plumed metadynamics potential is added to the AMBER potential
to run MD, is there a way for us to output the bias potential that has been
added through AMBER? This might save us the time to externally estimate the
bias potential that may have been added.
With Warm Regards,
----------------------------------------------
Siddharth Sonti
PhD Candidate
Ahn Lab - Kulkarni Group
Office: Bainer Hall, Room 2129B
Department of Chemical Engineering
University of California, Davis
Webpage: Siddharth Sonti - Academic
<
https://sites.google.com/ucdavis.edu/siddharthsonti-academic/home>
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Received on Thu Feb 13 2025 - 12:00:02 PST
