Re: [AMBER] Fw: Problem Regarding PMF Graph

From: Jason Swails <>
Date: Fri, 15 May 2015 05:27:19 -0400

On Fri, May 15, 2015 at 12:47 AM, Shubhadip Das <>

> Dear Sir,
> Thanks for your reply. One thing I could not able to
> understand why i have to reset the value of pmf is zero around 8 A^0 because
> my system's half box length is around 12.4 A^0. Please
> advice. Thanks in advance.

‚ÄčAdrian was simply stating that the zero-point energy does not matter at
all for the analysis of your free energy profile, since only energy
differences are important (i.e., the DELTA-G along the coordinate or the
barrier height at the transition state). WHAM sets the zero-point energy
of your PMF to the lowest energy it finds, which means that, by definition,
no point along the PMF will have a negative energy, and this is OK.

If you *want* the PMF to have negative free energies and to have the PMF go
to zero at long distances (like 8 A), you need to shift the PMF down by a
constant energy term (i.e., the energy at 8 A) in order to have the
zero-point energy where you want it. 8 A (as Adrian used in his email) is
halfway between your starting and ending distances. If instead you want
the PMF to go to zero at half the box length, then you're free to use 6.2
instead, but again, it really does not matter (as only differences along
the PMF have any meaning, and shifting the curve up or down has no effect
on those differences).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri May 15 2015 - 02:30:19 PDT
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