Re: about usage of eABF method

From: Giacomo Fiorin (
Date: Thu Jul 29 2021 - 08:10:47 CDT

Hello Vidhya, the presence of an electric field, which I assume to be
constant over time (it may or may not change across the simulation cell),
means an additional force for each atom. This force *will* be counted in
the PMF via different mechanisms, depending on what you use.

   - Traditional ABF measures the total atomic forces as part of the time
   integration scheme, and applies the thermodynamic integration (TI) method
   to these forces to compute a PMF. The external electric potential is thus
   included in the PMF in an exact manner.*sec:colvarbias_abf__;Iw!!DZ3fjg!qd5FTn7rSngKVUB05RcAwMkhlk8dTRj7LtesQia5X80XYJGoeQ_Tj5F0JIJjIfdJUw$
   - eABF, as well as nearly all other methods (metadynamics, umbrella
   sampling, SMD, ...) use the resulting trajectory of the variable to
   estimate the PMF. The external electric potential is thus *sampled*
   like all other terms of the PMF (both enthalpic and entropic).*sec:colvarbias_ti_ext_czar__;Iw!!DZ3fjg!qd5FTn7rSngKVUB05RcAwMkhlk8dTRj7LtesQia5X80XYJGoeQ_Tj5F0JIJWGlPkGw$

In either case, the external electric potential becomes part of the PMF,
and whether this is representative of a system where there is no such
potential, it is up to you. Only in the special case where you're
computing a PMF for a single atom using as CV its absolute position (i.e.
distance from a dummy atom or from a very large group that effectively
doesn't move) you may subtract the electric potential to have an
*approximate* idea of how the PMF would be without it.


On Thu, Jul 29, 2021 at 5:13 AM Vidhya Sankar <> wrote:

> Dear Namd users
> I ma applying Elecric field during My simulation for
> tranlocation of molecule through nano pore
> So it becomes Non Equlibrium MD . So can i apply eABF method to calculate
> free energy also it it suitable to apply eABF method
> Kindly give me clarification
> With High Regards
> S . Vidhya sankar

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