I haven't done it myself, but both of these methods appear as if they
could be implemented out of the box in gromacs.
On the use of orientational restraints and symmetry corrections in
alchemical free energy calculations. Mobley DL, Chodera JD, Dill KA.
http://www.ncbi.nlm.nih.gov/pubmed/16965052
Absolute Binding Free Energy Calculations Using Molecular Dynamics
Simulations with Restraining Potentials. Jiyao Wang, Yuqing Deng, and
Benoît Roux
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1578458/
Chris
-- original message --
I'm applying COM pull on a two-domain protein by fixing the distance between
the centers of mass of each domain with an umbrella potential. However, I
find that the domains can rotate so that the inner surfaces of each domain
are not parallel any more. How can I apply a rotational restraint so that
each domain doesn't rotate during simulation? Thanks in advance.
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