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

Stefan Hoorman stefhoor at gmail.com
Sun Sep 27 03:41:13 CEST 2009

> Stefan Hoorman wrote:
> > I simulate 400 ps for each window. I have a total of 20 windows. My
> 400 ps is relatively short, especially given the speed of current hardware
> and
> of Gromacs 4.0.  I generally see longer time periods in the literature.
> > histogram looks like a chromatographic peak ranging from 0.74 and 0.91
> Then you are not getting the separation you described before (>2.5 nm).  It
> looks like you are only pulling a distance of 0.17 nm total.
> > in the x axis and the count (y axis) goes up to 30000. Is there a way to
> > index my histogram.xvg or my profile.xvg file and send it to the gromacs
> > user's list? Or is it not necessary?
> The best way to send this information is to generate image files and post
> them
> to a free site where others can see them (photobucket, etc).  Up to you to
> determine whether its necessary.  At this point, I think you are just not
> getting what you think you are setting up.
> -Justin
> 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 the
histogram is a straight line parallel to the x axis set in zero. I 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 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.
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