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

[Victor Rosas Garcia]

OK, I'll get to work adding a few more windows.

Thanx Justin

2014-12-02 17:27 GMT-06:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> 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
>
> --
> ==================================================
>
> 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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