From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Wed May 13 2009 - 16:23:49 CDT
Hi Sebastian,
On Wed, May 13, 2009 at 3:48 PM, Sebastian Stolzenberg
<s.stolzenberg_at_gmail.com> 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
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