From: Nathan A. B. <ba...@ch...> - 2003-12-31 14:06:20
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Hi Jerry -- Did you use mpirun to launch APBS? If not, then I would expect the behavior you're describing. Thanks, Nathan Jerry Greenberg <jp...@sd...> (12-30-2003 08:02:02-0800): > > >Nathan: > >Is it correct that when I run apbs in parallel and ask for data grids >(potentials etc) that I will get N (identical) files if I run with N >processors? > > >Thanks, > >Jerry End of message from Jerry Greenberg. -- 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 |
From: Jerry G. <jp...@sd...> - 2003-12-31 14:06:03
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Nathan: Is it correct that when I run apbs in parallel and ask for data grids (potentials etc) that I will get N (identical) files if I run with N processors? Thanks, Jerry |
From: Clueless S. <clu...@gm...> - 2011-06-24 18:19:44
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Hello! I am currently running APBS using Command Prompt in Windows. And i was wondering how to write out "space" in the input file because whenever i try to run the commands that contain spaces, the program won't recognize it. For example, read mol pqr C:\APBS\test.pqr end (works) read mol pqr C:\Program Files\APBS\test.pqr end (does not work because there is a space between Program and Files) Thank you in advance for your help! Helen |
From: Baker, N. <Nat...@pn...> - 2011-06-25 18:29:01
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Hello - Unfortunately, path names with spaces aren't supported in the APBS input files. Thanks, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://kdi.pnnl.gov/bios/baker.stm From: Clueless Star [mailto:clu...@gm...] Sent: Friday, June 24, 2011 11:19 AM To: apb...@li... Subject: [Apbs-users] APBS Hello! I am currently running APBS using Command Prompt in Windows. And i was wondering how to write out "space" in the input file because whenever i try to run the commands that contain spaces, the program won't recognize it. For example, read mol pqr C:\APBS\test.pqr end (works) read mol pqr C:\Program Files\APBS\test.pqr end (does not work because there is a space between Program and Files) Thank you in advance for your help! Helen |
From: Matteo R. <mat...@un...> - 2011-06-27 15:05:15
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Dear All, I found a problem in the command "print apolForce solvated". I'm using apbs.1.3 binaries version on linux. the input file: read mol pdb in.pdb parm flat param.prm end APOLAR name solvated grid 0.3 0.3 0.3 mol 1 srfm sacc swin 0.3 press 0.2394 gamma 0.0085 srad 1.4 bconc 0.033428 sdens 100.0 dpos 0.2 temp 298.15 calcenergy total calcforce comps END print apolEnergy solvated end print apolForce solvated end quit The output will present first the results due to command "calcforce comps" ; here is a sample (call it resultA): CALCULATION #1 (solvated): APOLAR Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n gamma 0.000003 pressure 0.005420 bconc 0.032327 tot 0 -3.689e-02 4.107e-02 7.347e-04 sasa 0 2.630e+01 -2.240e+01 -2.821e+00 sav 0 2.437e+00 -2.107e+00 -5.742e-01 wca 0 7.302e-01 -9.152e-01 7.381e-02 tot 1 2.078e-03 5.281e-02 4.650e-02 sasa 1 3.400e+00 -1.571e+01 -1.355e+01 sav 1 -8.823e-01 -7.590e+00 -7.568e+00 wca 1 8.334e-02 -3.596e-01 -1.683e-01 Then will print the results from "print apolForce solvated end" , here a sample (resultB): print APOL force 1 (solvated) end Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n tot all -- Total force for system sasa 0 2.630054553254E+01 -2.240017154677E+01 -2.821219128051E+00 sav 0 2.436685640038E+00 -2.107114121288E+00 -5.742351381563E-01 wca 0 7.302339174972E-01 -9.151520697294E-01 7.381246259457E-02 tot 0 2.946746509008E+01 -2.542243773779E+01 -3.321641803613E+00 sasa 1 3.399915233088E+00 -1.571140952433E+01 -1.354686721755E+01 sav 1 -8.823078871030E-01 -7.589532381085E+00 -7.568364458294E+00 wca 1 8.333644735653E-02 -3.596460782089E-01 -1.683420919478E-01 tot 1 2.600943793341E+00 -2.366058798363E+01 -2.128357376779E+01 sasa, sav and wca values are the same in resultA and resultB, but while in resultA we have: tot = -sasa*gamma-sav*press-WCA*bconc in resultB we find: tot = sasa + sav + wca. This is probably due to a bug. regards, Matteo. ---------------------------------------------------------------------- SEMEL (SErvizio di Messaging ELettronico) - CSIT -Universita' di Udine |
From: Matteo R. <mat...@un...> - 2011-06-27 15:13:50
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Dear all, I checked agin my files and i noticed that I pasted the wrong input file. Here is the correct one: read mol pdb in.pdb parm flat param.prm end APOLAR name solvated grid 0.3 0.3 0.3 mol 1 srfm sacc swin 0.3 press 0.005420 gamma 0.000003 srad 1.4 bconc 0.032327 sdens 100.0 dpos 0.2 temp 298.15 calcenergy total calcforce comps END print apolEnergy solvated end print apolForce solvated end quit Regards, Matteo. ---------------------------------------------------------------------- SEMEL (SErvizio di Messaging ELettronico) - CSIT -Universita' di Udine |
From: Baker, N. <Nat...@pn...> - 2011-06-28 13:54:08
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Hi Matteo -- I'll work with Tucker to investigate this. Thanks, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://kdi.pnnl.gov/bios/baker.stm > -----Original Message----- > From: Matteo Rotter [mailto:mat...@un...] > Sent: Monday, June 27, 2011 7:49 AM > To: Baker, Nathan > Cc: apb...@li... > Subject: APBS apolar calculation > > Dear All, > > I found a problem in the command "print apolForce solvated". > I'm using apbs.1.3 binaries version on linux. > the input file: > > read > mol pdb in.pdb > parm flat param.prm > end > > APOLAR name solvated > grid 0.3 0.3 0.3 > mol 1 > srfm sacc > swin 0.3 > press 0.2394 > gamma 0.0085 > srad 1.4 > bconc 0.033428 > sdens 100.0 > dpos 0.2 > temp 298.15 > calcenergy total > calcforce comps > END > print apolEnergy solvated end > print apolForce solvated end > quit > > The output will present first the results due to command > "calcforce comps" ; here is a sample (call it resultA): > > CALCULATION #1 (solvated): APOLAR > Printing per atom forces (kJ/mol/A) > Legend: > tot n -- Total force for atom n > sasa n -- SASA force for atom n > sav n -- SAV force for atom n > wca n -- WCA force for atom n > > gamma 0.000003 > pressure 0.005420 > bconc 0.032327 > > tot 0 -3.689e-02 4.107e-02 7.347e-04 > sasa 0 2.630e+01 -2.240e+01 -2.821e+00 > sav 0 2.437e+00 -2.107e+00 -5.742e-01 > wca 0 7.302e-01 -9.152e-01 7.381e-02 > tot 1 2.078e-03 5.281e-02 4.650e-02 > sasa 1 3.400e+00 -1.571e+01 -1.355e+01 > sav 1 -8.823e-01 -7.590e+00 -7.568e+00 > wca 1 8.334e-02 -3.596e-01 -1.683e-01 > > Then will print the results from > "print apolForce solvated end" , here a sample (resultB): > > print APOL force 1 (solvated) end > Printing per atom forces (kJ/mol/A) > Legend: > tot n -- Total force for atom n > sasa n -- SASA force for atom n > sav n -- SAV force for atom n > wca n -- WCA force for atom n > tot all -- Total force for system > sasa 0 2.630054553254E+01 -2.240017154677E+01 -2.821219128051E+00 > sav 0 2.436685640038E+00 -2.107114121288E+00 -5.742351381563E-01 > wca 0 7.302339174972E-01 -9.151520697294E-01 7.381246259457E-02 > tot 0 2.946746509008E+01 -2.542243773779E+01 -3.321641803613E+00 > sasa 1 3.399915233088E+00 -1.571140952433E+01 -1.354686721755E+01 > sav 1 -8.823078871030E-01 -7.589532381085E+00 -7.568364458294E+00 > wca 1 8.333644735653E-02 -3.596460782089E-01 -1.683420919478E-01 > tot 1 2.600943793341E+00 -2.366058798363E+01 -2.128357376779E+01 > > sasa, sav and wca values are the same in resultA and resultB, but > while in resultA we have: tot = -sasa*gamma-sav*press-WCA*bconc > in resultB we find: tot = sasa + sav + wca. > This is probably due to a bug. > > regards, Matteo. > > > ---------------------------------------------------------------------- > SEMEL (SErvizio di Messaging ELettronico) - CSIT -Universita' di Udine |
From: Clueless S. <clu...@gm...> - 2011-06-24 17:59:06
|
Hello! I am currently running APBS using Command Prompt in Windows. And i was wondering how to write out "space" in the input file because whenever i try to run the commands that contain spaces, the program won't recognize it. For example, read mol pqr C:\APBS\test.pqr end (works) read mol pqr C:\Program Files\APBS\test.pqr end (does not work because there is a space between Program and Files) Thank you in advance for your help! Helen |