AMBER Archive (2008)

Subject: AMBER: Extracting the electric field (and its gradient) on particular solute atoms

From: John Chodera (
Date: Tue Apr 15 2008 - 19:36:01 CDT

Hello all,

I am working with Thomas la Cour Jansen on the calculation of 2DIR
spectra from simulations of peptides in explicit solvent. The method
Thomas is using (see Ref. [1]) requires we extract the electric field
vector and its spatial gradient (a 3x3 symmetric tensor) for a number
of backbone atoms every 20 fs along a dynamics simulation, to be
further processed by his analysis codes for the computation of spectra
from multi-point time correlation functions.

To be consistent with the way in which AMBER defines the potential
energy function, we would like to extract the electrostatic field at
these atomic sites neglecting the contribution from the charge on the
probe atom itself, as well as the charges on atoms separated by one or
two bonds. The contribution from atoms separated by three bonds
should also be scaled as specified by the forcefield.

The electric field vector can be easily extracted from the
electrostatic force on each atom, but the spatial gradient of this
field presents a little more difficulty. This will involve both
contributions from the direct Coulomb interactions and from the
reciprocal space contributions (interpolated from the grid). While
the expressions for these contributions are not complex, I could use
some guidance about (1) where precisely in the code these extra
calculations must be inserted, and (2) what variables contain the
information necessary for this calculation. It may just be my
unfamiliarity with the energy routines, but the portions of the code
responsible for the nonbonded calculations seem somewhat inscrutable
to me.

Any helpful suggestions that could be provided here would be very much

Many thanks,


[1] Jansen TLC, Knoester J. Nonadiabatic effects in the two-dimensional
infrared spectra of peptides: Application to alanine dipeptide. JPC B
110:22910, 2006.

Dr. John D. Chodera <>      | Mobile    : 415.867.7384
Postdoctoral researcher, Pande lab            | Lab phone : 650.723.1097
Department of Chemistry, Stanford University  | Lab fax   : 650.724.4021
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