You can split your trajectory in half, do an RMSF calculation using the
two half as independent trajectories, and report the range of RMSF
between the two trajs as an estimate of the errors.
Or do a better version of that using block averages perhaps.
Adrian
On 2/29/24 2:29 PM, Duggan, Brendan via AMBER wrote:
> [External Email]
>
> 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
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--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Thu Feb 29 2024 - 12:00:02 PST
