[gmx-users] gmx bar histogram data

Justin Lemkul jalemkul at vt.edu
Sun Mar 26 16:14:05 CEST 2017

On 3/23/17 3:16 PM, Eric Smoll wrote:
> Hello GROMACS users,
> I am using the "gmx bar" tool in GROMACS 5.1.2 and am interested in
> understanding the relevance of the histogram data output by the -oh flag.
> Dr. Lemkul provides a very helpful reference
> <http://www.sciencedirect.com/science/article/pii/0021999176900784?via%3Dihub>
> and a summary
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/07_analysis.html>
> which states:
> "in order to obtain a reliable estimate of ΔG, we need adequate sampling
> within each window (based on ∂H/∂λ distributions) and between neighboring
> windows (ΔH distributions). The significant overlap in the distributions of
> the data shown here and the low error estimate printed by gmx bar indicate
> that we have achieved this goal. If your own calculations give you
> non-overlapping histograms, resulting in large error estimates, then you
> likely either need longer simulations, more λ states, or better parameters
> for whatever molecule it is you are trying to transform."
> When using the (default) mdp setting calc_lambda_neighbours=1, I assume
> that the only overlap that matters is immediate-neighbour histogram
> overlap. For example, when examining deltaH histograms that track the
> "forward difference" lambda[i+1]-lambda[i], it only needs to show good
> overlap with the lambda[i+2]-lambda[i+1] and lambda[i]-lambda[i-1]
> histograms. Am I correct?




Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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