[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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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