AMBER Archive (2008)

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

From: Tom Darden (
Date: Wed Apr 16 2008 - 16:30:53 CDT

the field gradients are involved in forces where dipoles are used
that is, energy terms come from dipole dotted with field and forces from
dipole dotted against field gradient
Note the contribution to field and field gradients from other
atom's dipoles can be ignored if you have a charge only system---but you
can get the contribution from charges using the below codes:

  for the reciprocal part, look in
"grad_sum_dipolerc" in ew_dipole_recip.f
for the direct, look in
"short_ene_dip" inside short_ene.f
for the 1-4 fields and gradients, look in
"get_14_dipole" inside extra_pts.f
finally need to fix for valence terms (recall the reciprocal terms contain
1-1,1-2,1-3 and 1-4 terms, that either should be missing or scaled)
correction is in
"nb_adjust_dipole" in ew_force.f

this should at least get you started
tom d
On Tue, 15 Apr 2008, John Chodera wrote:

> 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
> appreciated.
> Many thanks,
> John
> [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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