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

Victor Rosas Garcia rosas.victor at gmail.com
Tue Dec 2 18:30:00 CET 2014

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:


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:


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):


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?

Best regards


2014-11-18 16:31 GMT-06:00 Victor Rosas Garcia <rosas.victor at gmail.com>:
> Thanks, I'll check it out.  It may be a remnant of a previous, botched, run.
> 2014-11-18 15:56 GMT-06:00 Justin Lemkul <jalemkul at vt.edu>:
>> On 11/18/14 3:23 PM, Victor Rosas Garcia wrote:
>>> Sorry about that Office messup.
>>> These are the new links:
>>> histogram
>>> https://drive.google.com/file/d/0B2K7fedV_ZFzaFlOMWh1QXFTa2s/view?usp=sharing
>>> profile
>>> https://drive.google.com/file/d/0B2K7fedV_ZFzSm16bnlJSUFGVms/view?usp=sharing
>>> I understand that the profile may not look exactly the same between
>>> different runs, but I do think the difference is large enough to think
>>> something is amiss.
>> Sampling in window 1 is a little odd - the distribution is incredibly
>> narrow, if you can even call it a distribution at all.  Make sure everything
>> is OK in that window.  In the absence of a well-defined minimum, you're not
>> going to get a sensible profile.  People's mileage varies as far as
>> recapitulating that PMF curve, but I have received confirmation from at
>> least two other people that the PMF can be reproduced following the method
>> in the paper.
>> -Justin
>> --
>> ==================================================
>> 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
>> http://mackerell.umaryland.edu/~jalemkul
>> ==================================================
>> --
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