2009/9/28 <[email protected]> > > Stefan Hoorman wrote: > > > > > 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. > > Then all your sampling is occurring in one window. That's your problem. I > don't know how you're generating your inputs for the different windows, but > likely something is going wrong there. > > > I will try pulling in only one direction then. Should have the results > > in a few days. > > Probably won't make a difference. The problem more likely lies in what > I've > described above. > > -Justin > > > Thank you >
To generate each window I use "trjconv -f original_separation_trajectory.xtc -s topol.tpr -dump time_where_specific_distance_is_found -o frame_where_separation_between_structures_is_x.gro" Once I have the coordinate files regarding this specific distance between my pull groups, I simulate each of them (using the same topol.top file, index.ndx...etc) but with the new md_pull.mdp file I've shown here earlier. Is this wrong for wham analysis? Thank you
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