## apbs-users

 [Apbs-users] A question regarding energy and grid size From: Ran Friedman - 2003-10-19 17:15:13 Attachments: Message as HTML ```Hi, I've tried to calculate the electrostatic properties of the same system (protein in water and salt) twice, using essentially the same settings except for the grid dimensions and number of points, as follows: run 1 ---- Grid dimensions: 161 x 161 x 161 Grid spacings: 0.400 x 0.400 x 0.400 Grid lengths: 64.000 x 64.000 x 64.000 Grid center: (9.745, 12.641, 21.402) run 2 ---- Grid dimensions: 193 x 193 x 193 Grid spacings: 0.333 x 0.333 x 0.333 Grid lengths: 64.000 x 64.000 x 64.000 Grid center: (9.745, 12.641, 21.402) The largest dimension of protein is 42 angstroms. Now as far as I understand it, I should expect that the results of run 1 shouldn't be too different than the results of run2. However, what I got was: run 1 ---- Total electrostatic energy = 1.551673825736E+05 kJ/mol run 2 ---- Total electrostatic energy = 2.042898691098E+05 kJ/mol Am I missing something? Does the number of levels have an influence on the energy results? Or should I expect better convergence when the grid is smaller? Thank you, Ran. -- ------------------------------------------------------ Ran Friedman Laser laboratory for fast reactions in biology Department of biochemistry Faculty of life sciences Tel-Aviv university 972-3-6409824 ------------------------------------------------------ ```
 Re: [Apbs-users] A question regarding energy and grid size From: Nathan A. Baker - 2003-10-20 14:27:50 ```Dear Dr. Friedman -- It sounds like you are not calculating energies with the "self-energy" terms removed. These terms arise from the inclusion of the energies of the non-delta-function charge distributions interacting with themselves and are standard sources of grid artifacts (as you describe below) in PB calculations. If you want to know the electrostatic energy of a protein in solution you should: 1) Calculate the solvation energy from the difference of the energies of a) System with different sdie and pdie values b) System with both sdie and pdie set to the protein dielectric 2) Add the Coulomb energy for the system of point charges in a medium with a dielectric constant of pdie. You can use apbs/tools/manip/coulomb for this. This procedure removes self-energies and is therefore much less sensitive to grid spacings, positions, etc. Thanks, Nathan Ran Friedman (10-19-2003 17:15:09+0200): >Hi, > >I've tried to calculate the electrostatic properties of the same system >(protein in water and salt) twice, using essentially the same settings >except for the grid dimensions and number of points, as follows: > >run 1 >---- > > Grid dimensions: 161 x 161 x 161 > Grid spacings: 0.400 x 0.400 x 0.400 > Grid lengths: 64.000 x 64.000 x 64.000 > Grid center: (9.745, 12.641, 21.402) > >run 2 >---- > > Grid dimensions: 193 x 193 x 193 > Grid spacings: 0.333 x 0.333 x 0.333 > Grid lengths: 64.000 x 64.000 x 64.000 > Grid center: (9.745, 12.641, 21.402) > >The largest dimension of protein is 42 angstroms. > >Now as far as I understand it, I should expect that the results of run 1 >shouldn't be too different than the results of run2. However, what I got >was: > >run 1 >---- >Total electrostatic energy = 1.551673825736E+05 kJ/mol > >run 2 >---- >Total electrostatic energy = 2.042898691098E+05 kJ/mol > >Am I missing something? Does the number of levels have an influence on >the energy results? Or should I expect better convergence when the grid >is smaller? > >Thank you, >Ran. > > >-- >------------------------------------------------------ >Ran Friedman >Laser laboratory for fast reactions in biology >Department of biochemistry >Faculty of life sciences >Tel-Aviv university >972-3-6409824 >------------------------------------------------------ > > End of message from Ran Friedman. -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 Phone: (314) 362-2040, Fax: (314) 362-0234 URL: http://www.biochem.wustl.edu/~baker PGP key: http://cholla.wustl.edu/~baker/pubkey.asc ```
 [Apbs-users] Visual. From: Diego Vallejo - 2003-11-26 22:58:00 Attachments: Message as HTML ```Hi, I want to display Electrostatic Potential contour map lines along with 3D raster models like Rasmol, MolMol, etc. of my molecule. Any [free] suggestion? The input is the stdout of APBS. (3D grid data) Thanks in advance. Diego Vallejo - vallejo@... ++++++++++++++++++++++ Instituto de Física de Líquidos y Sistemas Biológicos - UNLP/CONICET 59 Nº789 (B1900BTE) La Plata. + Tel: +54 221 425 4904/ 423 3283 #17 Fax: +54 221 425 7317 + -----Mensaje original----- De: apbs-users-admin@... [mailto:apbs-users-admin@...]En nombre de Ran Friedman Enviado el: Domingo, 19 de Octubre de 2003 12:15 p.m. Para: apbs-users@... Asunto: [Apbs-users] A question regarding energy and grid size Hi, I've tried to calculate the electrostatic properties of the same system (protein in water and salt) twice, using essentially the same settings except for the grid dimensions and number of points, as follows: run 1 ---- Grid dimensions: 161 x 161 x 161 Grid spacings: 0.400 x 0.400 x 0.400 Grid lengths: 64.000 x 64.000 x 64.000 Grid center: (9.745, 12.641, 21.402) run 2 ---- Grid dimensions: 193 x 193 x 193 Grid spacings: 0.333 x 0.333 x 0.333 Grid lengths: 64.000 x 64.000 x 64.000 Grid center: (9.745, 12.641, 21.402) The largest dimension of protein is 42 angstroms. Now as far as I understand it, I should expect that the results of run 1 shouldn't be too different than the results of run2. However, what I got was: run 1 ---- Total electrostatic energy = 1.551673825736E+05 kJ/mol run 2 ---- Total electrostatic energy = 2.042898691098E+05 kJ/mol Am I missing something? Does the number of levels have an influence on the energy results? Or should I expect better convergence when the grid is smaller? Thank you, Ran. -- ------------------------------------------------------ Ran Friedman Laser laboratory for fast reactions in biology Department of biochemistry Faculty of life sciences Tel-Aviv university 972-3-6409824 ------------------------------------------------------ --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.537 / Virus Database: 332 - Release Date: 06/11/2003 ```
 Re: [Apbs-users] Visual. From: Nathan A. Baker - 2003-11-30 17:14:38 ```Yes, you should be able to do this easily in the VMD software package (Schulten research group) -- you can use the apbs/tools/vmd direct6ory examples to guide you throught this. Also, the Sanner/Olson group at TSRI plan to release a version of PMV which supports APBS execution and visualization in teh near future. Thanks for using APBS. Sincerely, Nathan Baker Diego Vallejo (11-26-2003 18:10:26-0300): >Hi, > >I want to display Electrostatic Potential contour map lines along with 3D >raster models like Rasmol, MolMol, etc. of my molecule. Any [free] >suggestion? >The input is the stdout of APBS. (3D grid data) > >Thanks in advance. >Diego Vallejo - vallejo@... ++++++++++++++++++++++ >Instituto de Física de Líquidos y Sistemas Biológicos - UNLP/CONICET >59 Nº789 (B1900BTE) La Plata. + >Tel: +54 221 425 4904/ 423 3283 #17 Fax: +54 221 425 7317 + > > -----Mensaje original----- > De: apbs-users-admin@... >[mailto:apbs-users-admin@...]En nombre de Ran Friedman > Enviado el: Domingo, 19 de Octubre de 2003 12:15 p.m. > Para: apbs-users@... > Asunto: [Apbs-users] A question regarding energy and grid size > > > Hi, > I've tried to calculate the electrostatic properties of the same system >(protein in water and salt) twice, using essentially the same settings >except for the grid dimensions and number of points, as follows: > > run 1 > ---- > > Grid dimensions: 161 x 161 x 161 > Grid spacings: 0.400 x 0.400 x 0.400 > Grid lengths: 64.000 x 64.000 x 64.000 > Grid center: (9.745, 12.641, 21.402) > > run 2 > ---- > > Grid dimensions: 193 x 193 x 193 > Grid spacings: 0.333 x 0.333 x 0.333 > Grid lengths: 64.000 x 64.000 x 64.000 > Grid center: (9.745, 12.641, 21.402) > > The largest dimension of protein is 42 angstroms. > > Now as far as I understand it, I should expect that the results of run 1 >shouldn't be too different than the results of run2. However, what I got >was: > > run 1 > ---- > Total electrostatic energy = 1.551673825736E+05 kJ/mol > > run 2 > ---- > Total electrostatic energy = 2.042898691098E+05 kJ/mol > > Am I missing something? Does the number of levels have an influence on the >energy results? Or should I expect better convergence when the grid is >smaller? > > Thank you, > Ran. > > >-- >------------------------------------------------------ >Ran Friedman >Laser laboratory for fast reactions in biology >Department of biochemistry >Faculty of life sciences >Tel-Aviv university >972-3-6409824 >------------------------------------------------------ > > >--- >Outgoing mail is certified Virus Free. >Checked by AVG anti-virus system (http://www.grisoft.com). >Version: 6.0.537 / Virus Database: 332 - Release Date: 06/11/2003 End of message from Diego Vallejo. -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 Phone: (314) 362-2040, Fax: (314) 362-0234 URL: http://www.biochem.wustl.edu/~baker PGP key: http://cholla.wustl.edu/~baker/pubkey.asc ```
 RE: [Apbs-users] Visual. From: Diego Vallejo - 2003-12-01 23:54:09 ```Thanks Nathan, I'll give it a try and let you know. Saludos Diego -----Mensaje original----- De: apbs-users-admin@... [mailto:apbs-users-admin@...]En nombre de Nathan A. Baker Enviado el: Domingo, 30 de Noviembre de 2003 12:15 p.m. Para: Diego Vallejo CC: apbs-users@... Asunto: Re: [Apbs-users] Visual. Yes, you should be able to do this easily in the VMD software package (Schulten research group) -- you can use the apbs/tools/vmd direct6ory examples to guide you throught this. Also, the Sanner/Olson group at TSRI plan to release a version of PMV which supports APBS execution and visualization in teh near future. Thanks for using APBS. Sincerely, Nathan Baker Diego Vallejo (11-26-2003 18:10:26-0300): >Hi, > >I want to display Electrostatic Potential contour map lines along with 3D >raster models like Rasmol, MolMol, etc. of my molecule. Any [free] >suggestion? >The input is the stdout of APBS. (3D grid data) > >Thanks in advance. >Diego Vallejo - vallejo@... ++++++++++++++++++++++ >Instituto de Física de Líquidos y Sistemas Biológicos - UNLP/CONICET >59 Nº789 (B1900BTE) La Plata. + >Tel: +54 221 425 4904/ 423 3283 #17 Fax: +54 221 425 7317 + > --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.537 / Virus Database: 332 - Release Date: 06/11/2003 ```