collective variable space PMF, including biasing potential terms?

From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Wed May 13 2009 - 14:48:05 CDT

Dear All,

as far as I understand (with NAMD 2.7b1), there are two ways I can
measure potential of mean forces in collective variable space: ABF and
metadynamics.

1.)
For small systems like the alanine dipeptide, does one PMF method have
any performance advantages over the other?

2.)
Eventually, I want to add a few biasing dihedral energy terms and
measure the effect on its free energy surface.
Thus, I also need to include the biasing dihedral terms into the PMF
calculations.
One way to do this I see is using tclForces with the "addenergy" command
(adding the dihedral energy terms into the "MISC" bin).
Which method, ABF or metadynamics, takes into the account the MISC
energies for the PMF calculation?

Thank you,
Best,
Sebasitan

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