<br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Stefan Hoorman wrote:<br>
<br>
> I simulate 400 ps for each window. I have a total of 20 windows. My<br>
<br>
400 ps is relatively short, especially given the speed of current hardware and<br>
of Gromacs 4.0. I generally see longer time periods in the literature.<br>
<br>
> histogram looks like a chromatographic peak ranging from 0.74 and 0.91<br>
<br>
Then you are not getting the separation you described before (>2.5 nm). It<br>
looks like you are only pulling a distance of 0.17 nm total.<br>
<br>
> in the x axis and the count (y axis) goes up to 30000. Is there a way to<br>
> index my histogram.xvg or my profile.xvg file and send it to the gromacs<br>
> user's list? Or is it not necessary?<br>
<br>
The best way to send this information is to generate image files and post them<br>
to a free site where others can see them (photobucket, etc). Up to you to<br>
determine whether its necessary. At this point, I think you are just not<br>
getting what you think you are setting up.<br>
<br>
-Justin<br>
<br>
</blockquote></div>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.<br>
<br>