[gmx-users] Fluctuation properties

Pelin S Bulutoglu pbulutog at purdue.edu
Fri Sep 28 23:17:24 CEST 2018

Dear Dr. Spoel,

Thank you for your reply. Do you mean calculating fluctuation properties for different pieces of the energy file and calculating std deviation? I tried that but the std deviation changes depending on the length of the blocks that I use.


Pelin Su Bulutoglu

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of David van der Spoel <spoel at xray.bmc.uu.se>
Sent: Friday, September 28, 2018 4:37:42 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Fluctuation properties

Den 2018-09-28 kl. 21:18, skrev Pelin S Bulutoglu:
> Dear Gromacs users,
> How can I assess the uncertainty of the properties calculated with the -fluct_props option in gmx energy? Since these are fluctuation properties, I cannot make an error estimation such as block averaging. Any suggestion is appreciated.
You will have to do it manually for now by cutting your energy file in
pieces (well, use the -b and -e options).

> Regards,
> Pelin Su Bulutoglu
> Graduate Research Assistant
> School of Chemical Engineering
> Purdue University

David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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