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):
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 0 | Mol 1 | Mol 0 | Mol 1 | Mol 0 | Mol 1 | |
-3.00 | 0.0E+00 | 0.0E+00 | 0.0E+00 | 0.0E+00 | 0 | 0 |
-2.50 | 8.4E+00 | -1.3E+01 | 1.1E+02 | -1.1E+02 | 0 | 0 |
-2.00 | 3.8E+01 | -3.4E+01 | 8.2E+01 | -8.2E+01 | 0 | 0 |
-1.50 | 6.3E+01 | -5.5E+01 | 4.2E+01 | -4.0E+01 | 0 | 0 |
-1.00 | 8.8E+01 | -8.8E+01 | 4.2E+00 | -4.2E+01 | 0 | 0 |
-0.50 | 1.0E+02 | -1.0E+02 | -1.2E+01 | 1.6E+01 | 0 | 0 |
0.00 | 1.1E+02 | 0 | -2.1E+01 | 2.1E+01 | 0 | 0 |
0.50 | 9.6E+01 | -9.8E+01 | -1.1E+01 | 4.2E+00 | 0 | 0 |
1.00 | 8.4E+01 | -8.8E+01 | 4.2E+00 | 0.0E+00 | 0 | 0 |
1.50 | 6.7E+01 | -6.5E+01 | 6.3E+00 | 4.2E+00 | 0 | 0 |
2.00 | 5.3E+01 | -5.3E+01 | 6.3E+01 | 6.3E+01 | 0 | 0 |
2.50 | 4.6E+01 | -4.8E+01 | 6.3E+01 | -2.1E+01 | 0 | 0 |
3.00 | 3.8E+01 | -3.8E+01 | 6.3E+00 | -6.3E+00 | 0 | 0 |
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