[gmx-users] Histogram result in free energy calculation

Justin Lemkul jalemkul at vt.edu
Wed Jul 22 03:43:04 CEST 2015

On 7/20/15 10:15 AM, minky son wrote:
> Thank you for kind answer,
> After I ran the simulation, the all values resulted from Free energy
> calculation in Justin tutorial were almost same.
> But I have difficulty in drawing histogram using xmgrace. Whenever I draw
> the histogram, it showed totally different with the figure in tutorial..
> Recently the server was fixed. So the following link is working now:
> http://bio.gnu.ac.kr/~chip/
> Please give me any command to solve this problem.

The output is awkward because there are dissimilar distributions plotted 
altogether.  There are also weird output artifacts that lead to those huge 
spikes that throw off the plots.  Minor output issues, nothing related to the 
actual results.

You have to separate the distributions based on what they are (as you'll note in 
the tutorial).  Just dumping everything into XmGrace is useless.  Either parse 
the histogram.xvg file with a simple script to write separate files or hide the 
dissimilar distributions.



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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