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From: J.Dziedzic <J.Dziedzic@so...>  20091207 11:06:55

Hello! I am trying to utilize the apbs code to include implicit solvent in a DFT calculation. My system is represented by an electronic charge density (the "cloud") sampled on a fine grid and a set of positive point charges representing the atomic cores. The positions of the cores are passed to apbs via the pqr file. The electronic charge density is passed to apbs via a charge map. A suitably defined map of smoothly varying dielectric constant is passed to apbs via a diel map (three maps, actually). Ionic concentrations are all zero. MDH boundary conditions are used. Manual focusing is utilized with progressively finer meshes, but the physical grid size is unchanged (since the potential in the whole box, not just in the vicinity of the molecule, is required as output  see below). Apbs is then used to calculate the resulting potential map, which is output to a .dx file. This map is then read by the DFT code, replacing the Hartree potential of the DFT calculation (the potential due to the electron cloud). A new charge distribution resulting from this potential is then computed, passed to apbs and the cycle continues until energy convergence is reached. I have several doubts regarding the details of an apbs calculations that I hope you might answer. 1) Does inputting a charge density map invalidate the point charges supplied in the pqr file or are _both_ the point charges and the 'cloud' included in the calculation? I am assuming the latter. 2) Does the electrostatic potential produced by 'write pot' include the ions in any way or is it just due to the electron cloud (which is what I need)? If it includes the ions, does it make sense to run apbs with almostzero charges supplied in the pqr file to obtain the potential due to the cloud only? 3) What is the rationale for having a set of three shifted diel maps? If the grid spacing is very fine (0.075A), will supplying the same map file for all three maps be a reasonable approximation or will this make no sense whatsoever (I can imagine derivatives of diel being wrong then). 4) Since the atomic cores are now embedded in a medium with a varying dielectric constant, I can no longer use the Ewald technique in my DFT code to compute the corecore interaction energy. Is there any way I can obtain the corecore energy from apbs, i.e. the energy of interaction of the point charges supplied in the pqr file, embedded in a medium of varying diel, supplied as maps? What about the corecloud energy, is there any way to obtain this from apbs? 5) Is there any way to perform an apbs calculation with periodic boundary conditions for the potential? Thank you in advance,  J. Dziedzic 
From: Nathan Baker <baker@bi...>  20091208 14:21:04

Hello  > I have several doubts regarding the details of an apbs calculations > that I hope you might answer. > > 1) Does inputting a charge density map invalidate the point charges > supplied in the pqr file or are _both_ the point charges and the > 'cloud' included in the calculation? I am assuming the latter. You are correct: only the cloud is included in the calculation. > 2) Does the electrostatic potential produced by 'write pot' include > the ions in any way or is it just due to the electron cloud (which is > what I need)? If it includes the ions, does it make sense to run > apbs with almostzero charges supplied in the pqr file to obtain the > potential due to the cloud only? It should be due to the cloud only. > 3) What is the rationale for having a set of three shifted diel maps? > If the grid spacing is very fine (0.075A), will supplying the same > map file for all three maps be a reasonable approximation or will > this make no sense whatsoever (I can imagine derivatives of diel > being wrong then). You are correct: the three shifted maps are needed for derivative calculations. > 4) Since the atomic cores are now embedded in a medium with a varying > dielectric constant, I can no longer use the Ewald technique in my > DFT code to compute the corecore interaction energy. Is there > any way I can obtain the corecore energy from apbs, i.e. the > energy of interaction of the point charges supplied in the pqr > file, embedded in a medium of varying diel, supplied as maps? > What about the corecloud energy, is there any way to obtain > this from apbs? Yes, you can set up a free energy cycle to transfer the core charges to a homogeneous dielectric medium (and calculate the transfer energy) and then calculate the Coulombic energy of the core point charges in the homogeneous dielectric. > 5) Is there any way to perform an apbs calculation with periodic > boundary conditions for the potential? Unfortunately, not yet. We're (still) working on this! Thanks, Nathan > Thank you in advance, >  J. Dziedzic > > > >  > Return on Information: > Google Enterprise Search pays you back > Get the facts. > http://p.sf.net/sfu/googledev2dev > _______________________________________________ > apbsusers mailing list > apbsusers@... > https://lists.sourceforge.net/lists/listinfo/apbsusers — Nathan Baker (http://bakergroup.wustl.edu/) Associate Professor, Dept. of Biochemistry and Molecular Biophysics Director, Computational and Molecular Biophysics Graduate Program Center for Computational Biology, Washington University in St. Louis 
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