From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Tue Mar 31 2015 - 11:41:35 CDT
Hi Bala,
The Colvars module calculates the force of the system on your
transition coordinate based on the Cartesian forces on each atom
obtained from NAMD. I'm almost positive that the latter forces include
the external electric field.
Whether it makes sense to use ABF or not depends on whether your
system reaches equilibrium. If the system can't equilibrate or simply
doesn't equilibrate on a timescale shorter than your simulations, then
you won't be calculating correct free energy differences. For
instance, in a periodic box of NaCl solution with an applied field,
there is a net flow of ion current through the system. Such a flow
means that the electric force applied to the system is not
conservative—you don't have a well defined potential energy nor a well
defined potential of mean force. For systems such as nanopores under
an external field, it is common to have non-negligible hydrodynamic
flows in different parts of the system and frictional dissipation. See
for example
http://journals.aps.org/pre/abstract/10.1103/PhysRevE.78.021912
But all that said, if your system can reach equilibrium along all
coordinates (except for your transition coordinate), the potential of
mean force along that coordinate should be well defined. So for an
appropriately constructed system, you should be able to, for example,
calculate the potential of mean force for a single ion in an ion
channel under the influence of an external electric field.
Jeff
–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
On Tue, Mar 31, 2015 at 10:42 AM, Bala subramanian
<bala.biophysics_at_gmail.com> wrote:
> Hello friends,
>
> Suppose i do the ABF simulation along a reaction coordinate (For example the
> movement of a single ion along the z-direction) in the presence of external
> electric field (efield option in namd). How does NAMD calculate the force
> evaluations in the bins in such case, does it internally excludes the
> influence of the electric field.
>
> Precisely is it advisable to perform ABF in combination with an external
> electric field.
>
> Thanks,
> Bala
>
> --
> C. Balasubramanian
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