<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>
> Ok Justin, here are both profile and histogram files. Please let me know<br>
> if you can't get access or something like this. I have never used this<br>
> protobucket before.<br>
> "<a href="http://i784.photobucket.com/albums/yy123/stefhoor/wham_stefhoor/profile.jpg" target="_blank">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" target="_blank">http://i784.photobucket.com/albums/yy123/stefhoor/wham_stefhoor/histogram.jpg</a>"<br>
<br>
The histogram shows only one peak, indicating only one window, just beyond 1.0<br>
nm of COM separation. Is this an error in creating the plot, or is this really<br>
the result? Like I've said before, you should have many windows, with<br>
overlapping distributions in order to correctly extract PMF using WHAM.<br>
<br>
> And here are my pull code stuff that is inside my mdp files. The first<br>
> one (Pull Code 1) is the one I used to separate the structures, and the<br>
> following (Pull Code 2) is the one used to simulate each window.<br>
<br>
I hadn't noticed this before, and I don't know if it's meaningful, but it's<br>
worth looking into. You're pulling in two dimensions. I'm not sure the status<br>
of the WHAM implementation in g_wham, but it is more common in the literature to<br>
extract one-dimensional PMF, and this is the most commonly-used method. I would<br>
suggest orienting your system such that you are pulling directly along a single<br>
axis, and running things again.<br>
<br>
-Justin<br>
<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<br>
> post it, but if you think it is necessary I would be glad to post it as<br>
> well. Sorry about the distance, I inverted the 2.41 (wrote 2.14). My<br>
> separation is from starting position (close to 1nm) till 2.5. But since<br>
> the structures always move a little in the beginning of each window, I<br>
> guess the final maximum distance is 2.41.<br>
><br>
<a href="http://www.gromacs.org/search" target="_blank"></a><br></blockquote><div><br>Ok. The histogram is the actual result. As I said, my windows are all there, all the reaction coordinates I mentioned before are there to be analysed and in the correct order, but the result comes always the same way. This histogram is the actual result. <br>
I will try pulling in only one direction then. Should have the results in a few days.<br>Thank you <br></div></div><br>