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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--
========================================
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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