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

[Justin A. Lemkul]

Stefan Hoorman wrote:

> 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
> 
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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