2009/9/26 <gmx-users-requ...@gromacs.org> > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > 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. > > -Justin > Ok Justin, here are both profile and histogram files. Please let me know if you can't get access or something like this. I have never used this protobucket before. "http://i784.photobucket.com/albums/yy123/stefhoor/wham_stefhoor/profile.jpg " " http://i784.photobucket.com/albums/yy123/stefhoor/wham_stefhoor/histogram.jpg " And here are my pull code stuff that is inside my mdp files. The first one (Pull Code 1) is the one I used to separate the structures, and the following (Pull Code 2) is the one used to simulate each window. ; Pull Code 1 pull = umbrella pull_geometry = distance pull_dim = Y Y N pull_nstxout = 10 pull_nstfout = 1 pull_ngroups = 1 pull_group0 = Protein pull_group1 = SLC pull_vec1 = 1 1 0 pull_init1 = 0 pull_rate1 = 0.001 pull_k1 = 2000 pull_constr_tol = 1e-06 pull_pbcatom0 = 0 pull_pbcatom1 = 0
; Pull Code 2 pull = umbrella pull_start = yes pull_geometry = distance pull_dim = Y Y N pull_nstxout = 10 pull_nstfout = 1 pull_ngroups = 1 pull_group0 = Protein pull_group1 = SLC pull_vec1 = 1 1 0 pull_init1 = 0 pull_rate1 = 0 pull_k1 = 2000 pull_constr_tol = 1e-06 pull_pbcatom0 = 0 pull_pbcatom1 = 0 The rest of my mdp stuff is pretty standard so, to save space I didn't post it, but if you think it is necessary I would be glad to post it as well. Sorry about the distance, I inverted the 2.41 (wrote 2.14). My separation is from starting position (close to 1nm) till 2.5. But since the structures always move a little in the beginning of each window, I guess the final maximum distance is 2.41.
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