AMBER Archive (2006)

Subject: AMBER: reconstructing PMF

From: Ioana Cozmuta (icozmuta_at_mail.arc.nasa.gov)
Date: Mon Apr 10 2006 - 13:15:20 CDT

Hi Amber users,

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.
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.

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?

I would greatly appreciate your thoughts on the above matters.

Thank you,
Ioana 

-- 
Ioana Cozmuta, Ph.D
Eloret Corporation
NASA Ames Research Center
Mail Stop 230-3
Moffett Field, CA  94035
phone (650) 604-0993
e-mail: icozmuta_at_mail.arc.nasa.gov
http://people.nas.nasa.gov/~ioana/

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