Re: [AMBER] Ambiguity in PMF calculated from umbrella sampling of a dihedral angle

From: Jason Swails <>
Date: Tue, 1 Oct 2013 12:20:29 -0400

On Tue, Oct 1, 2013 at 9:11 AM, Mohan Pradhan <>wrote:

> Thanks for the suggestions Jason. But I reconfirmed that I have not
> reversed the X-axes. When I plot the dihedral angles sampled from the 2
> simulations (plots attached), I also see less sampling around the dihedral
> angles which correspond to the barriers in those PMF plots.

These two plots show the same information as the original two. I can think
of only two possible explanations:

1) You are not performing equilibrium sampling because your simulations are
too short and the snapshots are biased by the configurations generated
while relaxing to the 'new' location of the biasing potential (I say 'new'
since I assume you take the final snapshot of the previous window as the
starting coordinate for the next one).

2) You have somehow incorporated a 180 degree phase shift into your
measurement of the dihedral angles. This is deceptively easy to do given
the periodicity of torsion angles.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Oct 01 2013 - 09:30:08 PDT
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