Calculating a PMF using the free-energy code#
The free-energy coupling-parameter approach (see sec. Free energy calculations)
provides several ways to calculate potentials of mean force. A potential
of mean force between two atoms can be calculated by connecting them
with a harmonic potential or a constraint. For this purpose there are
special potentials that avoid the generation of extra exclusions,
see sec. Exclusions. When the position of the minimum or the constraint
length is 1 nm more in state B than in state A, the restraint or
constraint force is given by
Potentials of mean force can also be calculated using position
restraints. With position restraints, atoms can be linked to a position
in space with a harmonic potential (see Position restraints).
These positions can be made a function of the coupling parameter
-r
and -rb
options, respectively. One could use this
approach to do targeted MD; note that we do not encourage the use of
targeted MD for proteins. A protein can be forced from one conformation
to another by using these conformations as position restraint
coordinates for state A and B. One can then slowly change