[gmx-users] extra factor in PMF

Gavin Melaugh gmelaugh01 at qub.ac.uk
Thu Apr 19 13:28:58 CEST 2012

Hi all

According to some references

1) J. Chem. Phys, 128, 044106, (2008)
2) Comparison of Methods to Compute the Potential of Mean Force

Daniel Trzesniak, Anna-Pitschna E. Kunz, Wilfred F. van Gunsteren Prof.
Article first published online: 28 NOV 2006
DOI: 10.1002/cphc.200600527

There is an extra factor that has to be taken into account when
calculating the PMF. This extra factor (2kTln(r)) results from the
transformation from the 3N Cartesian coordinates to 3N internal
coordinates. In the case of a reaction coordinate defined by a distance
r between two species the Jacobian (r*2sin(theta)) of the transformation
for 3D to  1D leads to an extra term in the PMF.
Therefore the true PMF should be

PMF(true) = PMF(g_wham) + 2kTln(r)

This extra factor is only significant at lower values of the reaction
coordinate. My question is; Does g_wham take this into account ?



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