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

[Victor Rosas Garcia]

Hello everybody,

I'm back.  From the last time I tried this, I took all the
configurations (all 500) and did the npt_umbrella equilibration.
*Then* I was able to pick evenly spaced configurations (25 of them)
and ran the md_umbrella. This is my histogram (g_wham does not
complain about poor sampling anywhere):

https://drive.google.com/file/d/0B2K7fedV_ZFzRF9qd2FsMTdrSm8/view?usp=sharing

and my profile is still wrong

https://drive.google.com/file/d/0B2K7fedV_ZFzUTZ6ZW54QXR5a2s/view?usp=sharing

Perhaps I need to go up to 31 windows, like in the paper?

Any ideas are welcome.

Victot

2014-12-02 20:46 GMT-06:00 Victor Rosas Garcia <rosas.victor at gmail.com>:
> 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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