[gmx-developers] Writing the electric field (and its gradient) on particular atoms during an MD simulation

John Chodera jchodera at gmail.com
Tue Apr 15 02:00:21 CEST 2008


I am working with a collaborator (Thomas la Cour Jansen) who is
developing methods for computing 2DIR spectra from molecular dynamics
simulations, for purposes of comparison between simulations and
experiment.  His methods employ a number of functions parameterized by
(1) atomic coordinates, (2) the electric field impinging upon
particular atoms, and (3) gradient of this field with respect to the
position at which this field is measured.

For these methods to work with a multitude of forcefields in a
self-consistent way, it would be extremely useful if we could have
gromacs write out the electric field on these atoms (and its gradient)
every N steps.  To be consistent with the way in which energies and
gradients for forcefields like AMBER are computed, the electric field
computed at atom position i would exclude the contributions from atom
i itself and the direct-space Coulomb interaction from atoms separated
by one or two bonds, and the contribution from atoms separated by
three bonds would be scaled (by half, in the case of AMBER).

Most, if not all, of this information is presumably already computed
in the force/gradient routines.  We are trying to assess how much
effort it would be to extract this information and whether it is
possible for a mere human like me to make these changes, or if I would
need to appeal to one of Wise Developers to make such a modification.

Many thanks in advance,

- 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

More information about the gromacs.org_gmx-developers mailing list