## Re: [Apbs-users] Extracting potential at a given point

 Re: [Apbs-users] Extracting potential at a given point From: Nathan Baker - 2005-08-24 13:18:33 ```Hi Sandeep -- I think apbs/tools/mesh/value should do what you need. Since Todd has wrapped the Vgrid class in Python, this could also be accomplished via Python (see apbs/tools/python for examples). Thanks, Nathan --- Sandeep Somani wrote: > Hi > > Is there a way to extract the electrostatic potential at a given point > specified by the x,y,z coordinates ? > > basically some way of interpolating from neighboring grid points in case > the point does not fall on the grid points. > > I guess it can be done by post processing the dx file. any tool already > there ?! > > -sandeep > > > > _______________________________________________ > apbs-users mailing list > apbs-users@... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > -- Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Washington University in St. Louis http://cholla.wustl.edu ```

 [Apbs-users] Re: energy discrepency From: Nathan Baker - 2005-07-27 20:25:35 ```Hi Frank -- It's hard to answer your question without more information. Can you send the input & output for the calculation? One guess is that the "total energy" was calculated from the integral form of the free energy functional while the per-atom energies were calculated as terms of a charge-potential summation. Thanks, Nathan --- "Frank D. Ducheneaux" wrote: > Hi All, > > > I just ran a solvation calculation on a small molecule (21 atoms) and > asked > the program to return total electrostatic potential energy and per-atom > electrostatic potential energy. When I added up the per-atom energies, > they did not equal the total energy. Is this normal or do I need to > relearn common addition. If this is normal, why is the summation > approximately 249 KJ/mol greater than the total. Thanks in advance. > > > -- > Frank Ducheneaux > Caltech > Division of Chemistry > m/c 127-72 > Pasadena, CA 91125 > (626)395-2689 > > -- Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Washington University in St. Louis http://cholla.wustl.edu ```
 [Apbs-users] Re: energy discrepency From: Frank D. Ducheneaux - 2005-07-27 21:09:58 Attachments: apbs.in apbs.out 100_mul.pqr ```Nathan, Here are in the.in and .out files for the calculation as well as the .pqr file. On Wed, 27 Jul 2005, Nathan Baker wrote: > Hi Frank -- > > It's hard to answer your question without more information. Can you send the > input & output for the calculation? One guess is that the "total energy" was > calculated from the integral form of the free energy functional while the > per-atom energies were calculated as terms of a charge-potential summation. > > Thanks, > > Nathan > > --- "Frank D. Ducheneaux" wrote: > > > Hi All, > > > > > > I just ran a solvation calculation on a small molecule (21 atoms) and > > asked > > the program to return total electrostatic potential energy and per-atom > > electrostatic potential energy. When I added up the per-atom energies, > > they did not equal the total energy. Is this normal or do I need to > > relearn common addition. If this is normal, why is the summation > > approximately 249 KJ/mol greater than the total. Thanks in advance. > > > > > > -- > > Frank Ducheneaux > > Caltech > > Division of Chemistry > > m/c 127-72 > > Pasadena, CA 91125 > > (626)395-2689 > > > > > > > -- > Assistant Professor, Dept. of Biochemistry and Molecular Biophysics > Washington University in St. Louis > http://cholla.wustl.edu > -- Frank Ducheneaux Caltech Division of Chemistry m/c 127-72 Pasadena, CA 91125 (626)395-2689 ```
 Re: [Apbs-users] Re: energy discrepency From: Robert Konecny - 2005-07-28 20:33:33 ```Hi Frank, to get accurate per-atom energies you need to use 'chgm spl0' option - I believe. robert On Wed, Jul 27, 2005 at 12:09:55PM -0700, Frank D. Ducheneaux wrote: > Nathan, > > Here are in the.in and .out files for the calculation as well as the .pqr > file. > > > On Wed, 27 Jul 2005, Nathan Baker wrote: > > > Hi Frank -- > > > > It's hard to answer your question without more information. Can you send the > > input & output for the calculation? One guess is that the "total energy" was > > calculated from the integral form of the free energy functional while the > > per-atom energies were calculated as terms of a charge-potential summation. > > > > Thanks, > > > > Nathan > > > > --- "Frank D. Ducheneaux" wrote: > > > > > Hi All, > > > > > > > > > I just ran a solvation calculation on a small molecule (21 atoms) and > > > asked > > > the program to return total electrostatic potential energy and per-atom > > > electrostatic potential energy. When I added up the per-atom energies, > > > they did not equal the total energy. Is this normal or do I need to > > > relearn common addition. If this is normal, why is the summation > > > approximately 249 KJ/mol greater than the total. Thanks in advance. > > > > > > > > > -- > > > Frank Ducheneaux > > > Caltech > > > Division of Chemistry > > > m/c 127-72 > > > Pasadena, CA 91125 > > > (626)395-2689 > > > > > > > > > > > > -- > > Assistant Professor, Dept. of Biochemistry and Molecular Biophysics > > Washington University in St. Louis > > http://cholla.wustl.edu > > > > -- > Frank Ducheneaux > Caltech > Division of Chemistry > m/c 127-72 > Pasadena, CA 91125 > (626)395-2689 > read > mol pqr 100_mul.pqr > end > > # SOLVATED STATE > elec name 1 > mg-manual > dime 97 97 97 > nlev 4 > grid 0.25 0.25 0.25 > gcent mol 1 > mol 1 > lpbe > bcfl mdh > ion 1 0.000 2.0 > ion -1 0.000 2.0 > pdie 1.0 > sdie 78.54 > chgm spl2 > srfm smol > srad 1.4 > swin 0.3 > temp 298.15 > gamma 0.105 > calcenergy comps > calcforce no > end > > # REFERENCE STATE > elec name 2 > mg-manual > dime 97 97 97 > nlev 4 > grid 0.25 0.25 0.25 > gcent mol 1 > mol 1 > lpbe > bcfl mdh > ion 1 0.000 2.0 > ion -1 0.000 2.0 > pdie 1.0 > sdie 1.0 > chgm spl2 > srfm smol > srad 1.4 > swin 0.3 > temp 298.15 > gamma 0.105 > calcenergy comps > calcforce no > end > > # solvation energy > print energy 1 - 2 > end > > quit > asc_getToken: Error occurred (bailing out). > Vio_scanf: Format problem with input. > > > ---------------------------------------------------------------------- > APBS -- Adaptive Poisson-Boltzmann Solver > Version 0.3.2 > > Nathan A. Baker (baker@...) > Dept. Biochemistry and Molecular Biophysics > Center for Computational Biology > Washington University in St. Louis > > Additional contributing authors listed in the code documentation. > > Copyright (c) 2002-2004. Washington University in St. Louis. > All Rights Reserved. > Portions Copyright (c) 1999-2002. The Regents of the University of > California. > Portions Copyright (c) 1995. Michael Holst. > > This program is free software; you can redistribute it and/or modify > it under the terms of the GNU General Public License as published by > the Free Software Foundation; either version 2 of the License, or > (at your option) any later version. > > This program is distributed in the hope that it will be useful, > but WITHOUT ANY WARRANTY; without even the implied warranty of > MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the > GNU General Public License for more details. > > You should have received a copy of the GNU General Public License > along with this program; if not, write to the Free Software > Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA > ---------------------------------------------------------------------- > APBS uses PMG and FEtk to solve the Poisson-Boltzmann equation > numerically. FEtk and PMG are developed and maintained by the Holst > Research Group at UC San Diego. PMG is designed to solve the nonlinear > Poisson-Boltzmann equation and similar problems with linear space and > time complexity through the use of box methods, inexact Newton methods, > and algebraic multilevel methods. FEtk is designed to solve general > coupled systems of nonlinear partial differential equations accurately > and efficiently using adaptive multilevel finite element methods, > inexact Newton methods, and algebraic multilevel methods. More > information about PMG and FEtk may be found at ;. > ---------------------------------------------------------------------- > > > This executable compiled on Apr 14 2005 at 15:09:48 > > Parsing input file apbs.in... > Parsed input file. > Got PQR paths for 1 molecules > Reading PQR-format atom data from 100_mul.pqr. > 21 atoms > Centered at (1.344e-01, -5.317e-01, 1.262e-01) > Net charge -1.00e-04 e > Preparing to run 2 PBE calculations. > ---------------------------------------- > CALCULATION #1 (1): MULTIGRID > Setting up problem... > Vpbe_ctor: Using max ion radius (2 A) for exclusion function > Debye length: 0 A > Current memory usage: 152.964 MB total, 152.964 MB high water > Using cubic spline charge discretization. > Grid dimensions: 97 x 97 x 97 > Grid spacings: 0.250 x 0.250 x 0.250 > Grid lengths: 24.000 x 24.000 x 24.000 > Grid center: (0.134, -0.532, 0.126) > Multigrid levels: 4 > Molecule ID: 1 > Linearized traditional PBE > Multiple Debye-Huckel sphere boundary conditions > 2 ion species (0.000 M ionic strength): > 2.000 A-radius, 1.000 e-charge, 0.000 M concentration > 2.000 A-radius, -1.000 e-charge, 0.000 M concentration > Solute dielectric: 1.000 > Solvent dielectric: 78.540 > Using "molecular" surface definition; harmonic average smoothing > Solvent probe radius: 1.400 A > Temperature: 298.150 K > Surface tension: 0.105 kJ/mol/A^2 > Electrostatic energies will be calculated > Solving PDE (see io.mc* for details)... > Total electrostatic energy = 2.977005765593E+03 kJ/mol > Fixed charge energy = 2977.01 kJ/mol > Mobile charge energy = 0 kJ/mol > Dielectric energy = 2977 kJ/mol > Per-atom energies: > Atom 0: 2.973488943559E+02 kJ/mol > Atom 1: 1.072665013578E+02 kJ/mol > Atom 2: 1.160352122314E+03 kJ/mol > Atom 3: 2.067037922293E+02 kJ/mol > Atom 4: 7.492701420461E+01 kJ/mol > Atom 5: 2.856708708944E+02 kJ/mol > Atom 6: 3.451853480174E+02 kJ/mol > Atom 7: 3.744185543381E+01 kJ/mol > Atom 8: 2.712855212097E+01 kJ/mol > Atom 9: 2.739894140930E+01 kJ/mol > Atom 10: 4.944183503233E+01 kJ/mol > Atom 11: 2.435813197806E+01 kJ/mol > Atom 12: 5.252629002268E+01 kJ/mol > Atom 13: 2.947345110467E+02 kJ/mol > Atom 14: 4.407082190594E+01 kJ/mol > Atom 15: 3.392928383064E+01 kJ/mol > Atom 16: 3.380917954040E+01 kJ/mol > Atom 17: 2.616188081094E+01 kJ/mol > Atom 18: 3.335484580895E+01 kJ/mol > Atom 19: 2.912577239033E+01 kJ/mol > Atom 20: 3.533301014056E+01 kJ/mol > ---------------------------------------- > CALCULATION #2 (2): MULTIGRID > Setting up problem... > Vpbe_ctor: Using max ion radius (2 A) for exclusion function > Debye length: 0 A > Current memory usage: 152.964 MB total, 153.065 MB high water > Using cubic spline charge discretization. > Grid dimensions: 97 x 97 x 97 > Grid spacings: 0.250 x 0.250 x 0.250 > Grid lengths: 24.000 x 24.000 x 24.000 > Grid center: (0.134, -0.532, 0.126) > Multigrid levels: 4 > Molecule ID: 1 > Linearized traditional PBE > Multiple Debye-Huckel sphere boundary conditions > 2 ion species (0.000 M ionic strength): > 2.000 A-radius, 1.000 e-charge, 0.000 M concentration > 2.000 A-radius, -1.000 e-charge, 0.000 M concentration > Solute dielectric: 1.000 > Solvent dielectric: 1.000 > Using "molecular" surface definition; harmonic average smoothing > Solvent probe radius: 1.400 A > Temperature: 298.150 K > Surface tension: 0.105 kJ/mol/A^2 > Electrostatic energies will be calculated > Solving PDE (see io.mc* for details)... > Total electrostatic energy = 2.993876993606E+03 kJ/mol > Fixed charge energy = 2993.88 kJ/mol > Mobile charge energy = 0 kJ/mol > Dielectric energy = 2993.83 kJ/mol > Per-atom energies: > Atom 0: 2.966527141596E+02 kJ/mol > Atom 1: 1.052161403688E+02 kJ/mol > Atom 2: 1.183513626403E+03 kJ/mol > Atom 3: 2.070363139990E+02 kJ/mol > Atom 4: 7.455310262093E+01 kJ/mol > Atom 5: 2.835246290732E+02 kJ/mol > Atom 6: 3.440256096107E+02 kJ/mol > Atom 7: 3.742768682920E+01 kJ/mol > Atom 8: 2.818809684971E+01 kJ/mol > Atom 9: 2.798831659314E+01 kJ/mol > Atom 10: 4.852995367474E+01 kJ/mol > Atom 11: 2.487828949407E+01 kJ/mol > Atom 12: 5.175993769930E+01 kJ/mol > Atom 13: 2.897528827370E+02 kJ/mol > Atom 14: 4.432574366949E+01 kJ/mol > Atom 15: 3.470477820159E+01 kJ/mol > Atom 16: 3.485225377534E+01 kJ/mol > Atom 17: 2.698503512734E+01 kJ/mol > Atom 18: 3.387382095375E+01 kJ/mol > Atom 19: 2.961432304847E+01 kJ/mol > Atom 20: 3.574502009203E+01 kJ/mol > ---------------------------------------- > PRINT STATEMENTS > print energy 1 (1) - 2 (2) end > Local net energy (PE 0) = -1.687122801377E+01 kJ/mol > Global net energy = -1.687122801377E+01 kJ/mol > ---------------------------------------- > CLEANING UP AND SHUTTING DOWN... > Destroying force arrays. > No energy arrays to destroy. > Destroying multigrid structures. > Destroying 1 molecules > Final memory usage: 0.000 MB total, 153.065 MB high water > > > Thanks for using APBS! > > ATOM 1 C1 RES 444 -2.2128 -0.6209 -0.2839 -0.3359 1.9491 > ATOM 2 C2 RES 444 -0.9943 0.0992 -0.8753 0.2008 1.9491 > ATOM 3 O3 RES 444 -1.4417 1.3799 -1.2651 -0.6494 1.7023 > ATOM 4 C4 RES 444 0.1412 0.3147 0.1416 -0.2350 1.9491 > ATOM 5 C5 RES 444 1.2741 -0.7364 0.0700 -0.1402 1.9491 > ATOM 6 C6 RES 444 0.8104 -2.1461 0.4863 -0.3222 1.9491 > ATOM 7 C7 RES 444 2.4431 -0.2923 0.9725 -0.3195 1.9491 > ATOM 8 H8 RES 444 -2.9957 -0.6817 -1.0406 0.1299 1.5975 > ATOM 9 H9 RES 444 -1.9483 -1.6305 0.0250 0.1114 1.5975 > ATOM 10 H10 RES 444 -2.5952 -0.0730 0.5773 0.0946 1.5975 > ATOM 11 H11 RES 444 -0.6339 -0.4278 -1.7602 0.1245 1.5975 > ATOM 12 H12 RES 444 -0.2645 0.3589 1.1535 0.1010 1.5975 > ATOM 13 H13 RES 444 0.5887 1.2844 -0.0809 0.1343 1.5975 > ATOM 14 H14 RES 444 -1.7786 1.7582 -0.4294 0.3315 1.5975 > ATOM 15 H15 RES 444 1.6463 -0.7851 -0.9561 0.1157 1.5975 > ATOM 16 H16 RES 444 1.6658 -2.8217 0.5285 0.1130 1.5975 > ATOM 17 H17 RES 444 0.1057 -2.5396 -0.2458 0.1086 1.5975 > ATOM 18 H18 RES 444 0.3338 -2.1165 1.4672 0.1085 1.5975 > ATOM 19 H19 RES 444 3.2644 -1.0066 0.8970 0.1099 1.5975 > ATOM 20 H20 RES 444 2.1186 -0.2334 2.0126 0.1068 1.5975 > ATOM 21 H21 RES 444 2.8077 0.6865 0.6577 0.1116 1.5975 > _______________________________________________ > apbs-users mailing list > apbs-users@... > http://cholla.wustl.edu/mailman/listinfo/apbs-users ```
 [Apbs-users] Extracting potential at a given point From: Sandeep Somani - 2005-08-24 09:57:18 ```Hi Is there a way to extract the electrostatic potential at a given point specified by the x,y,z coordinates ? basically some way of interpolating from neighboring grid points in case the point does not fall on the grid points. I guess it can be done by post processing the dx file. any tool already there ?! -sandeep ```
 Re: [Apbs-users] Extracting potential at a given point From: Nathan Baker - 2005-08-24 13:18:33 ```Hi Sandeep -- I think apbs/tools/mesh/value should do what you need. Since Todd has wrapped the Vgrid class in Python, this could also be accomplished via Python (see apbs/tools/python for examples). Thanks, Nathan --- Sandeep Somani wrote: > Hi > > Is there a way to extract the electrostatic potential at a given point > specified by the x,y,z coordinates ? > > basically some way of interpolating from neighboring grid points in case > the point does not fall on the grid points. > > I guess it can be done by post processing the dx file. any tool already > there ?! > > -sandeep > > > > _______________________________________________ > apbs-users mailing list > apbs-users@... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > -- Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Washington University in St. Louis http://cholla.wustl.edu ```
 RE: [Apbs-users] Extracting potential at a given point From: Sandeep Somani - 2005-08-24 13:24:10 ```yes this is just what i needed :) Thnx! > -----Original Message----- > From: Nathan Baker [mailto:sobolevnrm@...] > Sent: Wednesday, August 24, 2005 7:19 PM > To: Sandeep Somani; 'APBS' > Subject: Re: [Apbs-users] Extracting potential at a given point > > > Hi Sandeep -- > > I think apbs/tools/mesh/value should do what you need. Since > Todd has wrapped the Vgrid class in Python, this could also > be accomplished via Python (see apbs/tools/python for examples). > > Thanks, > > Nathan > > --- Sandeep Somani wrote: > > > Hi > > > > Is there a way to extract the electrostatic potential at a > given point > > specified by the x,y,z coordinates ? > > > > basically some way of interpolating from neighboring grid points in > > case the point does not fall on the grid points. > > > > I guess it can be done by post processing the dx file. any tool > > already there ?! > > > > -sandeep > > > > > > > > _______________________________________________ > > apbs-users mailing list > > apbs-users@... > > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > > > > > > -- > Assistant Professor, Dept. of Biochemistry and Molecular > Biophysics Washington University in St. Louis http://cholla.wustl.edu > ```