[gmx-users] Re: Re: Re: Re: Re: Re: umbrella potential

[Stefan Hoorman]

2009/9/28 <gmx-users-request at gromacs.org>

>
> 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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