dear Giovanni, I'm a bit confused... due to Gauss theorem, doesn't all the [A] procedure boil down to be the integral of the ionic+electronic charge inside the vdW radius ... I'm not sure I got what the RESP proceure does..
stefano Quoting Giovanni La Penna <glapenna at iccom.cnr.it>: > > As for point charges, here is a small recipe for isolated > molecules (see below) for the ESP/RESP procedure [A]. > Reference is Bayly et al, J. Phys. Chem., 97, 10269 (1993). > Final point charges for organo-metallic molecules compare > fairly well with standard or published values. > Another possibility is to compute charges by integrating > over atomic basins built on the basis of QT-AIM (Bader) [B]. > > [A] > 1) From PW or CP, write into the restart > directory (I guess into the charge-density.dat file) > the electrostatic potential in place of electron > density. This requires a call before writefile > in CPV/cpr.f90 (in case of CP). Paolo Giannozzi > wrote the subroutine to do this in CP. It would be > nice to have it in some contrib space. > In the input, it is recommended to use > explicit ion_radius(i), especially if you > want to compare with other programs (like CPMD, > for which the default radii are all 1.2 bohr). > > 2) Once the restart is generated, postprocess > it with PP as to print the electron density > into a friendly format, like a gaussian-cube file. > This file will contain the electrostatic potential > on a 3d-grid. PP can process restart produced also > by CP, provided disk_io='high'. > > 3) Write your own program to map the 3d-grid on > the molecular solvent-accessible surface. This will consist in reading > the 3d-grid, reading the molecular surface produced > with vdw radii and a rolling probe, and finally > interpolate the potential at the surface point > using neighbour points in the grid. For the molecular > surface, I recommend an old program called NSC (numerical surface > calculation): > > Eisenhaber et al, J. Comput. Chem., 16, 273 (1995) > > WARNING: this latter step for non-periodic systems! > Non-periodicity is assumed in the ESP/RESP procedure, > that consists in fitting the electrostatic surface > potential with a LIMITED sum of Coulomb interactions. > > The interpolation can be very coarse, the entire method > is plenty of error sources. > The output of this procedure is a list with > x y z U > for each point of the molecular surface. > In case step 4 is performed with the aresp code > that was once part of Amber, the output for a water > molecule is: > > 3 1072 0 > -0.9982123E-32 0.0000000E+00 0.2313846E+00 > -0.2610123E-32 0.1494187E+01 -0.9255383E+00 > -0.1829851E-15 -0.1494187E+01 -0.9255383E+00 > -6.5264638e-01 2.0485851e+00 1.0162867e+00 1.6945994e+00 > -7.2948945e-01 2.4209246e+00 6.0282018e-01 1.7305686e+00 > ... > > where 3 is the number of atoms, 1072 is the number of surface points, > 0 is the net charge, the three following lines are the atomic coordinates > in bohr, and the following lines are x,y,z,U (bohr,kcal/mol) > for the 1072 surface points. This format was once produced > by Gaussian. > > 4) Finally, one of the RESP codes available can be used. > I used the original aresp code that was part of the Amber 4.1 > code. > I think it is not worth to develop the RESP part in QE, > but for sure steps 1-3 could be done relatively easily. > And maybe with a minimum-image based periodicity. > I really don't know how to do it, but I am available > for testing. > > [B] > This is simpler, but for reasons that will be apparent to > everybody in a few applications, it is rarely used. > > 1) Postprocess the restart with PP and write the electron density > on a fine 3d-grid (cube-file). The size of 10 pm associated > to a density energy-cutoff of 250 Ry is rather accurate. > > 2) Process this electron density cube-file with a real-space > QT-AIM code. I used: > > Sanville et al., J. Comp. Chem., 28, 899 (2007). > http://theory.cm.utexas.edu/bader/ > > Charge are in ACF.dat. > This works also for periodic systems (maybe only orthorhombic?). > Problems occur with polar X-H bonds or in all cases > where the zero-flux of density comes too close to atoms desribed > with pseudo-potentials. > > Maybe, this will help, > > Giovanni > > ============================================================ > Giovanni La Penna - National research council (Cnr) > Institute for chemistry of organo-metallic compounds (Iccom) > via Madonna del Piano 10, > I-50019 Sesto Fiorentino, Firenze, Italy > tel.: +39 055 522-5264, fax: +39 055 522-5203 > e-mail: glapenna at iccom.cnr.it - http://www.iccom.cnr.it/lapenna > skype: giovannilapenna > ============================================================ > > On Wed, 1 Dec 2010, David Grifith wrote: > >> Dear All >> >> >> I am trying to calculate the point charge and the point spin density on each >> atom of a unit cell, certainly "WITHOUT" considering a 3D vector which is >> ... > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/
