From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Mar 31 2015 - 13:16:15 CDT
Hello Jeff and Bala: an external force (tclForces, tclBC, SMD, or any other
restraints) *will not be counted* in the reported system force.
Presumably, this applies to the efield option as well.
My suggestion would be to do a 0-step MD simulation (run 0) with NAMD with
and without efield, enabling outputSystemForce to make sure.
On Tue, Mar 31, 2015 at 12:41 PM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
> 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
> 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.
> 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
> > movement of a single ion along the z-direction) in the presence of
> > 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
-- Giacomo Fiorin Assistant Professor of Research Institute for Computational Molecular Science (ICMS) College of Science and Technology, Temple University 1925 North 12th Street (035-07), Room 704D Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 https://icms.cst.temple.edu/members.html http://giacomofiorin.github.io/
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