Thanks Adrian. I will split my trajectory up and calculate means and uncertainties from the groups.
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
________________________________
From: Adrian Roitberg via AMBER <amber.ambermd.org>
Sent: Thursday, February 29, 2024 11:42 AM
To: amber.ambermd.org <amber.ambermd.org>
Subject: Re: [AMBER] uncertainty in atomic positional fluctuations
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
> 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
> https://urldefense.com/v3/__http://sopnmr.ucsd.edu/__;!!LLK065n_VXAQ!hvXxCfS0oaFFZAQ329oeO0J1RojrgMhmBH78-RQOTZIEQbwYquJXKvLJNT9ONxUDr3kcoB3cTOl7OSv4iA$
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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
352-392-6972
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Received on Fri Mar 01 2024 - 12:00:02 PST
