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

[Ragnarok sdf]

>
>
>
> > 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?
>
> This should be right, hence my confusion about the histogram.  Are you sure
> there's only one peak?  Have you looked at it with a text editor?  There
> should
> be multiple entries in the file, one for each window that you're
> simulating?
>
> -Justin
>
> > Thank you
>

I've looked at the histogram file and it seems a bit complicated for me to
explain so I've taken the liberty to posting into rapidshare. Plese tell me
if you prefer another way for me to show you the file. Here goes the link:
"http://rapidshare.com/files/286048522/histo.xvg.html"
Thank you
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090928/9adcd9c2/attachment.html>