APBS ion pmf test case

$Id: README.html 1440 2009-11-17 20:37:08Z yhuang01 $

This is the two-ion test case for force evaluation from the Im et al. Comput. Phys. Commun. 111, 59--75 (1998) paper. The output of these run(s) are solvation energies for ion pairs (convert to total energy by adding Coulombic forces) and solvation force components. Molecule 0 is fixed (at x=-3) and molecule 1 was moved.

To run this test case, simply type ./runme.sh, making sure that the apbs binary is in your path.

Here's the output you can look for (all forces in kJ/mol/Å):

sasa
Solvent-accessible surface area force (scaled by the surface tension, gamma). NOTE THAT THIS FORCE HAS CHANGED! We're now using SASA forces instead of the spline-surface square gradient forces used in previous examples (and by Im et al).
qf
Reaction field force
db
Dielectric boundary force
ib
Ionic boundary force (osmotic pressure)

Here are the force results visually estimated from the Im et al paper (see above) with forces in kJ/mol/Å with one ion fixed at x = -3.0 Å.

Mol 1 location QF DB IB
Mol 0Mol 1 Mol 0Mol 1 Mol 0Mol 1
-3.00 0.0E+000.0E+00 0.0E+000.0E+00 00
-2.50 8.4E+00-1.3E+01 1.1E+02-1.1E+02 00
-2.00 3.8E+01-3.4E+01 8.2E+01-8.2E+01 00
-1.50 6.3E+01-5.5E+01 4.2E+01-4.0E+01 00
-1.00 8.8E+01-8.8E+01 4.2E+00-4.2E+01 00
-0.50 1.0E+02-1.0E+02 -1.2E+011.6E+01 00
0.00 1.1E+020 -2.1E+012.1E+01 00
0.50 9.6E+01-9.8E+01 -1.1E+014.2E+00 00
1.00 8.4E+01-8.8E+01 4.2E+000.0E+00 00
1.50 6.7E+01-6.5E+01 6.3E+004.2E+00 00
2.00 5.3E+01-5.3E+01 6.3E+016.3E+01 00
2.50 4.6E+01-4.8E+01 6.3E+01-2.1E+01 00
3.00 3.8E+01-3.8E+01 6.3E+00-6.3E+00 00

Here are the results from APBS 1.2.1:

x = 1.000

polarforces
  qf  0  8.398640174377E+01  9.818386932509E-06  9.795992245139E-06
  ib  0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  db  0  6.148361411050E+00  2.004819530432E-05  3.920937680245E-05
  tot 0  9.013476315482E+01  2.986658223683E-05  4.900536904759E-05
  qf  1  -8.466424236099E+01 -9.207442514897E-06 -2.534008066980E-05
  ib  1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  db  1  2.882747163943E+00  1.731862480409E-05  3.267273838847E-05
  tot 1  -8.178149519705E+01 8.111182289197E-06  7.332657718672E-06
  tot all 8.353267957774E+00 3.797776452602E-05  5.633802676626E-05

apolarforces
  sasa  0  -1.099776974333E+01  0.000000000000E+00  0.000000000000E+00
  sav   0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  wca   0  -5.826577086437E-01  -2.766670515801E-05  -2.766670515838E-05
  tot   0  -1.158042745197E+01  -2.766670515801E-05  -2.766670515838E-05
  sasa  1  1.111862435589E+01  0.000000000000E+00  0.000000000000E+00
  sav   1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  wca   1  5.826560767576E-01  -2.767485007143E-05  -2.767485007183E-05
  tot   1  1.170128043265E+01  -2.767485007143E-05  -2.767485007183E-05
  tot all  1.208529806779E-01  -5.534155522944E-05  -5.534155523021E-05

  Global net ELEC energy = -1.125191531404E+03 kJ/mol

Here are the results from APBS 1.2:

x = 1.000

polarforces
  qf  0  8.398640174377E+01  9.818386932509E-06  9.795992245139E-06
  ib  0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  db  0  6.148361411050E+00  2.004819530432E-05  3.920937680245E-05
  tot 0  9.013476315482E+01  2.986658223683E-05  4.900536904759E-05
  qf  1  -8.466424236099E+01 -9.207442514897E-06 -2.534008066980E-05
  ib  1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  db  1  2.882747163943E+00  1.731862480409E-05  3.267273838847E-05
  tot 1  -8.178149519705E+01 8.111182289197E-06  7.332657718672E-06
  tot all 8.353267957774E+00 3.797776452602E-05  5.633802676626E-05

apolarforces
  sasa  0  -1.099776974333E+01  0.000000000000E+00  0.000000000000E+00
  sav   0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  wca   0  -5.826577086437E-01  -2.766670515801E-05  -2.766670515838E-05
  tot   0  -1.158042745197E+01  -2.766670515801E-05  -2.766670515838E-05
  sasa  1  1.111862435589E+01  0.000000000000E+00  0.000000000000E+00
  sav   1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  wca   1  5.826560767576E-01  -2.767485007143E-05  -2.767485007183E-05
  tot   1  1.170128043265E+01  -2.767485007143E-05  -2.767485007183E-05
  tot all  1.208529806779E-01  -5.534155522944E-05  -5.534155523021E-05

  Global net ELEC energy = -1.125191531404E+03 kJ/mol

Here are the results from APBS 1.1.0:

x = 1.000

polarforces
  qf  0  8.398636786524E+01  3.277928951109E-05  2.248755327954E-05
  ib  0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  db  0  6.148315264050E+00  6.212090029364E-05  9.765261473306E-05
  tot 0  9.013468312929E+01  9.490018980473E-05  1.201401680126E-04
  qf  1  -8.466453877446E+01  1.260694683844E-05  -2.688056989348E-05
  ib  1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  db  1  2.882714236549E+00  9.382342500375E-05  1.225207937768E-04
  tot 1  -8.178182453791E+01  1.064303718422E-04  9.564022388330E-05
  tot all 8.352858591379E+00  2.013305616469E-04  2.157803918959E-04

apolarforces
  sasa  0  -1.099776974333E+01  0.000000000000E+00  0.000000000000E+00
  sav   0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  wca   0  -5.826577086437E-01  -2.766670515801E-05  -2.766670515838E-05
  tot   0  -1.158042745197E+01  -2.766670515801E-05  -2.766670515838E-05
  sasa  1  1.111862435589E+01  0.000000000000E+00  0.000000000000E+00
  sav   1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  wca   1  5.826560767576E-01  -2.767485007143E-05  -2.767485007183E-05
  tot   1  1.170128043265E+01  -2.767485007143E-05  -2.767485007183E-05
  tot all  1.208529806779E-01  -5.534155522944E-05  -5.534155523021E-05

  Global net ELEC energy = -1.125192402906E+03 kJ/mol

Here are the results from APBS 0.5.0:

x = -3.000
  sasa 0 2.014e-01 0.000e+00 0.000e+00
  sasa 1 2.014e-01 0.000e+00 0.000e+00
  sasa  0  2.014243542734E-01  0.000000000000E+00  0.000000000000E+00
  qf  0  2.402694548782E-01  1.193684463475E-04  9.707135192876E-05
  qf  1  2.402694548782E-01  1.193684463475E-04  9.707135192876E-05
  db  0  -1.040061396733E+00  5.059871689052E-05  1.004179762749E-04
  db  1  -1.040061396733E+00  5.059871689052E-05  1.004179762749E-04
  ib  0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  ib  1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  Global net ELEC energy = -1.494109084160E+03 kJ/mol
  Global net APOL energy = 1.073537020853E-01 kJ/mol
x = -2.500
  sasa 0 -1.047e+01 0.000e+00 0.000e+00
  sasa 1 1.088e+01 0.000e+00 0.000e+00
  sasa  0  -1.047406642222E+01  0.000000000000E+00  0.000000000000E+00
  qf  0  9.670776686682E+00  3.067299706303E-05  8.525779585775E-06
  qf  1  -9.776393142038E+00  1.160701475502E-04  9.737743502613E-05
  db  0  1.128766544950E+02  4.216378707828E-05  1.156092840465E-04
  db  1  -1.018562119621E+02  1.332582044569E-04  2.007546725043E-04
  ib  0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  ib  1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  Global net ELEC energy = -1.453172513724E+03 kJ/mol
  Global net APOL energy = 1.127544530116E-01 kJ/mol
x = -2.000
  sasa 0 -1.088e+01 0.000e+00 0.000e+00
  sasa 1 1.092e+01 0.000e+00 0.000e+00
  sasa  0  -1.087691513076E+01  0.000000000000E+00  0.000000000000E+00
  qf  0  3.600129707630E+01  1.673257382577E-05  -3.172493445854E-06
  qf  1  -3.698431978276E+01  1.362593318370E-04  1.348136933229E-04
  db  0  7.641808295612E+01  8.426812747154E-05  1.501550525155E-04
  db  1  -7.630995607470E+01  1.930747292853E-04  2.577078768374E-04
  ib  0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  ib  1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  Global net ELEC energy = -1.395864905308E+03 kJ/mol
  Global net APOL energy = 1.202783777713E-01 kJ/mol
x = -1.50
  sasa 0 -1.055e+01 0.000e+00 0.000e+00
  sasa 1 1.064e+01 0.000e+00 0.000e+00
  sasa  0  -1.055463616393E+01  0.000000000000E+00  0.000000000000E+00
  qf  0  6.263390243427E+01  -1.039272251661E-05  -3.653632695350E-05
  qf  1  -6.274351718559E+01  6.171199346571E-05  3.641783990404E-05
  db  0  4.141531409141E+01  8.939020846417E-05  1.464873997274E-04
  db  1  -3.980350645690E+01  1.618242786613E-04  2.096874862673E-04
  ib  0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  ib  1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  Global net ELEC energy = -1.343413508063E+03 kJ/mol
  Global net APOL energy = 1.278197055953E-01 kJ/mol
x = -1.00
  sasa 0 -1.104e+01 0.000e+00 0.000e+00
  sasa 1 1.080e+01 0.000e+00 0.000e+00
  sasa  0  -1.103805461418E+01  0.000000000000E+00  0.000000000000E+00
  qf  0  8.602515079485E+01  1.679958402518E-05  -1.286070388760E-06
  qf  1  -8.589474499290E+01  4.904393981795E-05  2.948346215562E-05
  db  0  5.146620466700E+00  1.263326043428E-04  1.972642536915E-04
  db  1  -2.462461594184E+00  1.419028113702E-04  2.025478366045E-04
  ib  0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  ib  1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  Global net ELEC energy = -1.297718358292E+03 kJ/mol
  Global net APOL energy = 1.354538497618E-01 kJ/mol
x = -0.500
  sasa 0 -1.088e+01 0.000e+00 0.000e+00
  sasa 1 1.080e+01 0.000e+00 0.000e+00
  sasa  0  -1.087691513076E+01  0.000000000000E+00  0.000000000000E+00
  qf  0  1.011157426881E+02  3.495539842345E-05  2.650020071179E-05
  qf  1  -1.018411965567E+02  2.379958570171E-05  7.021000073448E-06
  db  0  -1.147809320720E+01  1.908780322530E-04  2.832722451268E-04
  db  1  2.221256509495E+01  1.621554833141E-04  2.462408961005E-04
  ib  0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  ib  1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  Global net ELEC energy = -1.253921668205E+03 kJ/mol
  Global net APOL energy = 1.431402031209E-01 kJ/mol
x = 0.000
  sasa 0 -1.047e+01 0.000e+00 0.000e+00
  sasa 1 1.055e+01 0.000e+00 0.000e+00
  sasa  0  -1.047406642222E+01  0.000000000000E+00  0.000000000000E+00
  qf  0  1.076485044405E+02  4.150254188932E-05  2.584327997210E-05
  qf  1  -1.076452387179E+02  1.116736665075E-05  -1.918731685710E-05
  db  0  -2.164756414609E+01  1.200915665417E-04  1.684440777983E-04
  db  1  2.928788039760E+01  1.264642983339E-04  1.736212475138E-04
  ib  0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  ib  1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  Global net ELEC energy = -1.211966318316E+03 kJ/mol
  Global net APOL energy = 1.508265564799E-01 kJ/mol
x = 0.500
  sasa 0 -1.072e+01 0.000e+00 0.000e+00
  sasa 1 1.059e+01 0.000e+00 0.000e+00
  sasa  0  -1.071577564735E+01  0.000000000000E+00  0.000000000000E+00
  qf  0  1.027354991386E+02  2.555484206199E-05  1.063932308940E-05
  qf  1  -1.027864740990E+02  4.081203889223E-05  2.562624208050E-05
  db  0  -1.024263914547E+01  6.237801032056E-05  9.677805192977E-05
  db  1  4.694564975253E+00  7.269351372102E-05  1.062464666717E-04
  ib  0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  ib  1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  Global net ELEC energy = -1.169410509835E+03 kJ/mol
  Global net APOL energy = 1.585419149460E-01 kJ/mol
x = 1.000
  sasa 0 -1.100e+01 0.000e+00 0.000e+00
  sasa 1 1.112e+01 0.000e+00 0.000e+00
  sasa  0  -1.099776974333E+01  0.000000000000E+00  0.000000000000E+00
  qf  0  8.398636786523E+01  3.277928825388E-05  2.248755650954E-05
  qf  1  -8.466453877447E+01  1.260694492290E-05  -2.688056972615E-05
  db  0  6.148315264050E+00  6.212090033654E-05  9.765261477356E-05
  db  1  2.882714236549E+00  9.382342501820E-05  1.225207938255E-04
  ib  0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  ib  1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  Global net ELEC energy = -1.125192402906E+03 kJ/mol
  Global net APOL energy = 1.661992631981E-01 kJ/mol
x = 1.500
  sasa 0 -1.068e+01 0.000e+00 0.000e+00
  sasa 1 1.072e+01 0.000e+00 0.000e+00
  sasa  0  -1.067549077649E+01  0.000000000000E+00  0.000000000000E+00
  qf  0  6.661368503641E+01  3.283120005903E-05  2.336264942404E-05
  qf  1  -6.687857770544E+01  3.794378201242E-07  -4.537653753875E-05
  db  0  7.100467586189E+00  6.377840082367E-05  1.004771191938E-04
  db  1  3.082008432733E+00  1.019851332113E-04  1.318438583362E-04
  ib  0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  ib  1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  Global net ELEC energy = -1.087409226682E+03 kJ/mol
  Global net APOL energy = 1.739378257498E-01 kJ/mol
x = 2.000
  sasa 0 -1.092e+01 0.000e+00 0.000e+00
  sasa 1 1.096e+01 0.000e+00 0.000e+00
  sasa  0  -1.091720000162E+01  0.000000000000E+00  0.000000000000E+00
  qf  0  5.395122212118E+01  3.402365136823E-05  2.463252404579E-05
  qf  1  -5.435238595073E+01  2.345850272885E-05  5.498720638168E-06
  db  0  7.099496363901E+00  6.338076881104E-05  9.960971260094E-05
  db  1  1.822551374452E+00  7.422787937764E-05  1.097869885768E-04
  ib  0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  ib  1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  Global net ELEC energy = -1.056724540553E+03 kJ/mol
  Global net APOL energy = 1.814733525524E-01 kJ/mol
x = 2.500
  sasa 0 -1.072e+01 0.000e+00 0.000e+00
  sasa 1 1.068e+01 0.000e+00 0.000e+00
  sasa  0  -1.071577564735E+01  0.000000000000E+00  0.000000000000E+00
  qf  0  4.454222472665E+01  3.558462567387E-05  2.660491501258E-05
  qf  1  -4.504040092314E+01  -1.044092908553E-05  -3.622045970037E-05
  db  0  7.053724444849E+00  6.155505900578E-05  9.694085460358E-05
  db  1  -2.309382970894E+00  6.271891825021E-05  9.531078126617E-05
  ib  0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  ib  1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  Global net ELEC energy = -1.032072744366E+03 kJ/mol
  Global net APOL energy = 1.893047314465E-01 kJ/mol
x = 3.000
  sasa 0 -1.092e+01 0.000e+00 0.000e+00
  sasa 1 1.051e+01 0.000e+00 0.000e+00
  sasa  0  -1.091720000162E+01  0.000000000000E+00  0.000000000000E+00
  qf  0  3.737527031761E+01  3.343902445084E-05  2.403559379423E-05
  qf  1  -3.737539015853E+01  4.414820479892E-05  3.441749305654E-05
  db  0  7.008341960925E+00  6.385969683875E-05  1.003016820956E-04
  db  1  -7.008312180867E+00  7.315905619890E-05  1.101572582696E-04
  ib  0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  ib  1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  Global net ELEC energy = -1.011312542835E+03 kJ/mol
  Global net APOL energy = 1.969446766344E-01 kJ/mol
x = 3.500
  sasa 0 -1.064e+01 0.000e+00 0.000e+00
  sasa 1 1.068e+01 0.000e+00 0.000e+00
  sasa  0  -1.063520590564E+01  0.000000000000E+00  0.000000000000E+00
  qf  0  3.179181222228E+01  3.472564738899E-05  2.566914250463E-05
  qf  1  -3.259379322155E+01  1.216664204331E-05  -2.497181119826E-05
  db  0  6.969782295514E+00  6.257908926389E-05  9.840967875397E-05
  db  1  7.904107869827E+00  8.728726024045E-05  1.158752820808E-04
  ib  0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  ib  1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  Global net ELEC energy = -9.936580311110E+02 kJ/mol
  Global net APOL energy = 2.046252289721E-01 kJ/mol
x = 4.000
  sasa 0 0.000e+00 0.000e+00 0.000e+00
  sasa 1 0.000e+00 0.000e+00 0.000e+00
  sasa  0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  qf  0  2.736006693935E+01  3.271235623929E-05  2.341325695619E-05
  qf  1  -2.776033811952E+01  8.396915386866E-06  -3.668786316582E-05
  db  0  6.937279812724E+00  6.412225118915E-05  1.008451446546E-04
  db  1  1.489454481196E+00  1.060308624524E-04  1.379944549983E-04
  ib  0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  ib  1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
  Global net ELEC energy = -9.786249660218E+02 kJ/mol
  Global net APOL energy = 2.091848317949E-01 kJ/mol