[gmx-users] extra factor in PMF
martin.hoefling at googlemail.com
Wed Apr 25 12:05:40 CEST 2012
The factor depends on the choice of your reaction coordinate, and since
g_wham doesn't care about it - it's not included.
It accounts for the change in volume when going from cartesian to
general coordinates and can be computed as -k_B * T * (d ln ( | J |) /
d_lambda), where lambda is the function of atomic coordinates and | J |
the determinant of the Jacobian matrix.
(C. Chipot and A. Pohorille, editors. Free Energy Calculations: Theory
in Chemistry and Biology. Springer Series in Chemical Physics (Springer),
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