Hi Anthony,
just one remark here: Make sure you have always a couple of histograms
overlapping each other (maybe 5-10). If every histogram overlaps only
with two neighbors, you will severely underestimate the error.
Hence, to estimate the error, you need rather many histograms from many
short umbrella simulations than few histograms from few long umbrella
simulations.
Cheers,
Jochen
Am 2/3/13 11:43 AM, schrieb Nash, Anthony:
Hi Justin,
Thanks for the reply. You were spot on about the version difference.
Thanks again.
Anthony
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin Lemkul [jalem...@vt.edu]
Sent: 02 February 2013 18:06
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_wham missing option
On 2/2/13 12:58 PM, Nash, Anthony wrote:
Hi All,
I am using Gromacs 4.5.5 and running free energy calculations. According to the article
"g_wham - A Free Weighted Histogram......" (J. Chem. Theory. Comput. 2010, 6,
3713-3720), there is the option -bs-method. However, I am unable to find this option when
running g_wham. I want to use bayesian bootstraps of complete histograms.
I have a feeling I am missing something completely obvious. Any help would be
appreciated.
Take a closer look at g_wham -h. The option you're asking about is definitely
there. Also be sure you're using the version you think you are; g_wham was
overhauled between 4.0.7 and 4.5.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Dr. Jochen Hub
Computational Molecular Biophysics Group
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Georg-August-University of Göttingen
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