Re: reconstructing PMF

From: Jérôme Hénin (
Date: Thu Apr 13 2006 - 04:10:48 CDT

Hi Ioana,

> I have a trajectory in which I pull a DNA molecule through a 40A long
> channel (nanopore) using steered molecular dynamics (harmonic potential,
> constant velocity pulling). I did reconstruct the PMF from these
> simulations using Jarzynski's inequality.
> Alternatively, however I would like to use a technique that uses
> equilibrium simulations to reconstruct the PMF. For this reason I've
> taken frames from the SMD trajectory corresponding to a 0.1A movement of
> the center of mass of the molecule along the reaction coordinate and
> I've run for each of these frames full (equilibrium) MD.
DId you apply a bias on these simulations? If not, it is very likely that the
system has drifted away from its initial position, at least in some cases,
and I would be surprised if you achieved a good sampling of the pathway along
the pore in these runs. In the traditional way of doing this, umbrella
sampling, you would add harmonic biases that confine the system in a
particular region of the channel, and then stitch the resulting histograms
together to compute the PMF.

> Is there any standard methodology that I could use to reconstruct the
> free energy profile/PMF combining the SMD data with the additional
> information from the equilibrium MD simulations? Initially I thought
> that I could calculated the potential energies from each of the
> individual MD simulations, use a Boltzmann weight (so that states with
> low energy are emphasized more) and then input these energies into the
> PMF calculations.
As far as I can see, the only information you can easily extract from there is
an average potential energy profile.

> My second question is related to the SMD simulations and the way the
> external potential is distributed over the pulled atoms. It is my
> understanding that in the constant velocity or constant force pulling
> the external potential is applied to the center of mass of the molecule.
> However it would seem that the atoms that only the atoms following the
> center of mass are being pulled while the atoms that precede the center
> of mass are being pushed. Is this really the way SMD is implemented or
> is the force acting on COM being distributed such that the effect on all
> atoms is that of being pulled?
What is the difference between atoms being "pushed" and "pulled"?


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