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