Re: finding free energy at a time step using abf

From: Jerome Henin (
Date: Wed Jun 27 2007 - 13:56:14 CDT

Hi Rachel,
It depends how you define the free energy at a given timestep. If you
want it to be the value of the (converged) PMF at the current value of
the reaction coordinate, you just need to output the current value of
the RC and do some post-processing using the converged PMF at the end
of the simulations.
Note that it not clear to me what information you can extract from
such an RMSD/free energy plot. Just be aware that it is not at all the
same as a "free energy profile as a function of the RMSD" where the
RMSD would be the reaction coordinate.

On 6/27/07, <> wrote:
> I would like to be able to compare the abf free energy calculations to other
> data generated during the simulation (in particular the dcd file) with the final
> goal of being able to graph rmsd v. free energy. Is there something I can put
> in my configuration file so that I get an output that has the free energy
> calculated at each time step?
> Thanks for your time,
> Rachel Smith

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