AMBER Archive (2008)

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

From: John Chodera (jchodera_at_gmail.com)
Date: Wed Apr 16 2008 - 17:15:19 CDT

Tom,

Thanks! This is extremely helpful, and just what we need to get
started. It does indeed look like all the machinery we need is in
there -- it's just a matter of invoking it all in the right place
without interfering with normal operation. :)

Thanks again,

- John 

--
Dr. John D. Chodera <jchodera_at_gmail.com>      | Mobile    : 415.867.7384
Postdoctoral researcher, Pande lab            | Lab phone : 650.723.1097
Department of Chemistry, Stanford University  | Lab fax   : 650.724.4021
http://www.dillgroup.ucsf.edu/~jchodera

On 16/04/2008, Tom Darden <darden_at_niehs.nih.gov> wrote:
> john
>  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 <jchodera_at_gmail.com>      | Mobile    : 415.867.7384
> > Postdoctoral researcher, Pande lab            | Lab phone : 650.723.1097
> > Department of Chemistry, Stanford University  | Lab fax   : 650.724.4021
> > http://www.dillgroup.ucsf.edu/~jchodera
> >
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