[gmx-users] Re: WHAM

lloyd riggs lloyd.riggs at gmx.ch
Fri Mar 9 14:41:24 CET 2012

Dear All,

I went through and did some initial things with WHAM, and found the following.

if I use pullf the calculated free energy change, and change over time makes a nice perfect hemi parabolic graph that fits all the data in our and other labs.

if I use the pullx I get a graph of a zero line up unto a point halfway through the trajectories (and distance moved), which then starts at a peak equal to the correct free energy change of the entire run from the pullf, but then goes down to zero rapidlly over the rest of the run (ie the graph has a reversed shape, and peaks mid trajectory instead of at the end?).  If I just use the total free energy change, they match? 

Could somone explain to me why so I dont have to scramble through too much code (the math used) to figure it out...


Stephan Watkins
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