<br><br><div class="gmail_quote">2009/9/28 <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;">
<br>
Stefan Hoorman wrote:<br>
<br>
><br>
> Ok. The histogram is the actual result. As I said, my windows are all<br>
> there, all the reaction coordinates I mentioned before are there to be<br>
> analysed and in the correct order, but the result comes always the same<br>
> way. This histogram is the actual result.<br>
<br>
Then all your sampling is occurring in one window. That's your problem. I<br>
don't know how you're generating your inputs for the different windows, but<br>
likely something is going wrong there.<br>
<br>
> I will try pulling in only one direction then. Should have the results<br>
> in a few days.<br>
<br>
Probably won't make a difference. The problem more likely lies in what I've<br>
described above.<br>
<br>
-Justin<br>
<br>
> Thank you<br>
</blockquote></div><br>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"<br>
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.<br>
Is this wrong for wham analysis?<br>Thank you<br>