[gmx-users] extra factor in PMF

Martin Hoefling 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
and Applications
in Chemistry and Biology. Springer Series in Chemical Physics (Springer),
Best wishes


More information about the gromacs.org_gmx-users mailing list