I have submitted a manuscript where I reported some atomic positional fluctuations calculated using cpptraj. A reviewer has asked me to provide "statistical uncertainties for the statistical observables extracted from the simulation trajectories, e.g., RMSF". I don't see an easy way to obtain uncertainties on the APFs reported by cpptraj. I imagine it could be done by using cpptraj to align the structures, calculating average positions for the atoms, then measuring the distances so that means and standard deviations could be calculated, but I suspect that this what cpptraj is doing anyway. Am I missing something? Is there an easier way to do this?
Brendan M. Duggan, PhD
NMR Facility Director and Project Scientist
Skaggs School of Pharmacy and Pharmaceutical Sciences
University of California, San Diego
9255 Pharmacy Lane, MC 0657
La Jolla CA 92093-0657
office phone: (858) 534-8763
cell phone: (858) 692-2298
email: bmduggan.ucsd.edu
http://sopnmr.ucsd.edu
http://sopnmr.blogspot.com
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Received on Thu Feb 29 2024 - 12:00:02 PST
