[gmx-users] Wrong profile obtained in umbrella sampling tutorial

Justin Lemkul jalemkul at vt.edu
Wed Dec 3 00:28:00 CET 2014

On 12/2/14 12:29 PM, Victor Rosas Garcia wrote:
> Hello everybody,
> I'm back.
> I have redone part of the tutorial, re-equilibrated the configurations
> using the npt-umbrella.mdp, and then the umbrella sampling. I do
> notice that, even though my initial configurations were evenly spaced,
> after the NPT equilibration they move somewhat, so the histogram shows
> a couple of gaps. Please find the histograms image:
> https://drive.google.com/file/d/0B2K7fedV_ZFzeDlxM1pxdmV5bk0/view?usp=sharing
> the histograms show that I am getting again a *very* narrow
> distribution for the first window. Actually, it looks to me like half
> of the peak, as if the left side of the peak was not plotted.  Could
> it be because I am not very proficient in using xmgrace? The plotting
> command is "xmgrace -nxy histo1.xvg"
> The final profile I get looks the same as before, this is the link:
> https://drive.google.com/open?id=0B2K7fedV_ZFzTnoydHpyQm1OcHc&authuser=0
> The profile shows two deep drops in the regions where the histograms leave gaps.
> In addition, I have the terminal output of g_wham obtained with the -v
> flag (warning: it is an 11MB text file):
> https://drive.google.com/open?id=0B2K7fedV_ZFzYU1XcXphVUVyQ28&authuser=0
> Is it correct that the final configuration is moved with respect to
> the pre-equilibration configuration?
> Should I do a longer NPT equilibration of the initial configurations?

This is a normal outcome of most umbrella sampling, especially when using 
relatively few windows, as in the tutorial.  The best solution is just to go 
back and add a few windows centered around the regions of the reaction 
coordinate where there is no sampling.  The gaps in the distributions are 
throwing off the profile.  The half-distribution is a little bizarre, but seems 
at least consistent with the boundaries determined by g_wham; there is zero 
sampling below 0.47 nm, so the distribution reflects that fact.



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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