[gmx-users] Re: Re: Re: umbrella potential

Justin A. Lemkul jalemkul at vt.edu
Sun Sep 27 03:50:48 CEST 2009

Stefan Hoorman wrote:

> Well, I tried again, this time simulating 1ns each window. I thought 
> about simulating more, but thought of making a test before making longer 
> simulations for nothing. And again, my histogram looks like a 
> chromatographic peak, but the range this time is different. The rest of 

You should have overlapping roughly Gaussian distributions.  I can't tell if 
that's what you have, or if you have independent peaks.  If the latter is the 
case, then your windows do not overlap sufficiently to run WHAM.

> the histogram is a straight line parallel to the x axis set in zero. I 

Parallel lines indicate discontinuities in the WHAM analysis.  I really think 
you need to post an image of this online so we can see.  Without seeing what 
you're dealing with, it's very hard to be helpful.

> didn't understand what you meant by "getting what you think you are 
> setting up". I have checked the distance between my groups, both with 
> g_dist and by visual aid. The separate all right, there is no doubt 
> about that. Each window is what it should be, a window for the 1.5nm 
> distance starts at 1.5, decreases a little bit in the first picoseconds 
> and then stabilizes at 1.47 or 1.45. When I start g_wham analysis, the 
> verbose states that my initial distance is 0.99nm and then it says that 
> "Determined boundaries to 1.046511 and 2.140948". I tried this time 

Right, because your windows appear to range between these two values, so the 
closest window is restraining your structures at roughly 1 nm, and the furthest 
window is restraining the strucutres at 2.14 nm COM separation.  Is this what 
you expect?  I thought before you were dealing with distances out to 2.5 nm.

> simulating longer periods, and got the same result as before. The 
> profile graphic stars as a descending curve from 0 to -5 kCal, then it 
> starts rising in a "up the hill" way until it reaches +45kCal. I really 
> don't know what I am doing wrong this time.

Can you re-post the .mdp options you're using for pulling?  Also, images of both 
your histogram and profile would be extremely helpful.  I'm having a hard time 
picturing what you're describing with respect to the histograms.


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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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