Re: collective variable space PMF, including biasing potential terms?

From: Roman Petrenko (
Date: Wed May 13 2009 - 17:00:49 CDT

By the way, is fep implemented in cuda-version of namd?

On Wed, May 13, 2009 at 5:23 PM, Jerome Henin <> wrote:
> Hi Sebastian,
> On Wed, May 13, 2009 at 3:48 PM, Sebastian Stolzenberg
> <> wrote:
>> 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?
> In short, there is nothing obvious one way or the other. The full
> story is pretty complicated, and it isn't properly documented in the
> literature.
>> 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?
> Metadynamics will, since it only relies on the actual dynamics of the
> collective variables. You don't even have to tell NAMD about the
> biasing energy term. Just apply the biases, and that will show up in
> metadynamics. The "MISC" term has essentially no physical consequences
> in NAMD - it is mostly meant to make the output more informative.
> Best,
> J

Roman Petrenko
Physics Department
University of Cincinnati

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