<br><br><div class="gmail_quote">2009/9/26 <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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Stefan Hoorman wrote:<br>
<br>
> Well, I tried again, this time simulating 1ns each window. I thought<br>
> about simulating more, but thought of making a test before making longer<br>
> simulations for nothing. And again, my histogram looks like a<br>
> chromatographic peak, but the range this time is different. The rest of<br>
<br>
You should have overlapping roughly Gaussian distributions. I can't tell if<br>
that's what you have, or if you have independent peaks. If the latter is the<br>
case, then your windows do not overlap sufficiently to run WHAM.<br>
<br>
> the histogram is a straight line parallel to the x axis set in zero. I<br>
<br>
Parallel lines indicate discontinuities in the WHAM analysis. I really think<br>
you need to post an image of this online so we can see. Without seeing what<br>
you're dealing with, it's very hard to be helpful.<br>
<br>
> didn't understand what you meant by "getting what you think you are<br>
> setting up". I have checked the distance between my groups, both with<br>
> g_dist and by visual aid. The separate all right, there is no doubt<br>
> about that. Each window is what it should be, a window for the 1.5nm<br>
> distance starts at 1.5, decreases a little bit in the first picoseconds<br>
> and then stabilizes at 1.47 or 1.45. When I start g_wham analysis, the<br>
> verbose states that my initial distance is 0.99nm and then it says that<br>
> "Determined boundaries to 1.046511 and 2.140948". I tried this time<br>
<br>
Right, because your windows appear to range between these two values, so the<br>
closest window is restraining your structures at roughly 1 nm, and the furthest<br>
window is restraining the strucutres at 2.14 nm COM separation. Is this what<br>
you expect? I thought before you were dealing with distances out to 2.5 nm.<br>
<br>
> simulating longer periods, and got the same result as before. The<br>
> profile graphic stars as a descending curve from 0 to -5 kCal, then it<br>
> starts rising in a "up the hill" way until it reaches +45kCal. I really<br>
> don't know what I am doing wrong this time.<br>
><br>
<br>
Can you re-post the .mdp options you're using for pulling? Also, images of both<br>
your histogram and profile would be extremely helpful. I'm having a hard time<br>
picturing what you're describing with respect to the histograms.<br>
<br>
-Justin<br></blockquote><div>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.<br>"<a href="http://i784.photobucket.com/albums/yy123/stefhoor/wham_stefhoor/profile.jpg">http://i784.photobucket.com/albums/yy123/stefhoor/wham_stefhoor/profile.jpg</a>"<br>
"<a href="http://i784.photobucket.com/albums/yy123/stefhoor/wham_stefhoor/histogram.jpg">http://i784.photobucket.com/albums/yy123/stefhoor/wham_stefhoor/histogram.jpg</a>"<br>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.<br>
; Pull Code 1<br>pull = umbrella<br>pull_geometry = distance<br>pull_dim = Y Y N<br>pull_nstxout = 10<br>pull_nstfout = 1<br>pull_ngroups = 1<br>pull_group0 = Protein<br>pull_group1 = SLC<br>pull_vec1 = 1 1 0<br>
pull_init1 = 0<br>pull_rate1 = 0.001<br>pull_k1 = 2000<br>pull_constr_tol = 1e-06<br>pull_pbcatom0 = 0<br>pull_pbcatom1 = 0<br><br>; Pull Code 2<br>pull = umbrella<br>pull_start = yes<br>pull_geometry = distance<br>
pull_dim = Y Y N<br>pull_nstxout = 10<br>pull_nstfout = 1<br>pull_ngroups = 1<br>pull_group0 = Protein<br>pull_group1 = SLC<br>pull_vec1 = 1 1 0<br>pull_init1 = 0<br>pull_rate1 = 0<br>pull_k1 = 2000<br>pull_constr_tol = 1e-06<br>
pull_pbcatom0 = 0<br>pull_pbcatom1 = 0<br><br>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.<br>
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