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-- Dr. John D. Chodera <jchodera.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.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.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 > > > ----------------------------------------------------------------------- > > The AMBER Mail Reflector > > To post, send mail to amber.scripps.edu > > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu > > > > > ----------------------------------------------------------------------- > The AMBER Mail Reflector > To post, send mail to amber.scripps.edu > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu > ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Fri Apr 18 2008 - 21:19:55 PDT