> > Stefan Hoorman wrote: > > > 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 > " > > The histogram shows only one peak, indicating only one window, just beyond > 1.0 > nm of COM separation. Is this an error in creating the plot, or is this > really > the result? Like I've said before, you should have many windows, with > overlapping distributions in order to correctly extract PMF using WHAM. > > > 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. > > I hadn't noticed this before, and I don't know if it's meaningful, but it's > worth looking into. You're pulling in two dimensions. I'm not sure the > status > of the WHAM implementation in g_wham, but it is more common in the > literature to > extract one-dimensional PMF, and this is the most commonly-used method. I > would > suggest orienting your system such that you are pulling directly along a > single > axis, and running things again. > > -Justin > > > ; 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. > > > <http://www.gromacs.org/search> >
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. I will try pulling in only one direction then. Should have the results in a few days. Thank you
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