<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;"><br>
> Hi again. I have finished my wham analysis and here is what came out.<br>
> Well, first let me remind you of what we have already talked about. I<br>
> have simulated my system, comprised of protein and ligand, with the pull<br>
> code set to umbrella in order to obtain the entry structures for the<br>
> sampling simulations for my wham analysis. Now, after several<br>
> suggestions I have finally come up with a set of parameters that seemed<br>
> to work. I have included the "pull_start = yes " in my windows'<br>
> parameter file and have also increased the "pull_force" from 35 to<br>
> 2000. This increase seems to be sufficient to maintain my structures<br>
> restrained in the initial position, so now my distance between groups<br>
> float around a given value, which is quite close to the initial one. The<br>
> structures obtained for the wham windows were obtained selecting frames<br>
> in which a given distance between the structures was met. The structures<br>
> were obtained with a 0.1nm distance delta.<br>
> The problem now is the following. According to my .edr file, I should<br>
> have no more interaction (LJ-SR and Coul-SR) between my structures<br>
> starting from 2.5nm distance between them. So I would expect that my<br>
> profile.xvg file resulting from g_wham would give my values that would,<br>
> from 2.5nm on, kind of stabilize. My profile.xvg resulting from g_wham<br>
> gives me increasing values of umbrella potential starting in -1.1kcal<br>
> mol\S-1\N until +90kcal mol\S-1\N.<br>
> It does not look like anything I have seen for similar studies on the<br>
> literature. It has no minimum valey, i.e., the minimum value is the<br>
> first one and then the values just increase from there.<br>
> Thank you<br>
><br>
<br>
How long are you sampling in each window? How many total windows do you have?<br>
What do the histograms look like?<br>
<br>
-Justin<br>
<br>
</blockquote></div>I simulate 400 ps for each window. I have a total of 20 windows. My histogram looks like a chromatographic peak ranging from 0.74 and 0.91 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?<br>
Thank you<br>