APBS ion pmf test case

$Id: README.html,v 1.2 2002/06/03 15:48:12 apbs Exp $



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 edit the runme to provide the correct value for the variable bindir (where your APBS binary is located) and type ./runme.

Here's the output you can look for in the individual output files

"Total force on atom ..."
For the first calculation, this is the force (kJ/mol/A) on the given atom in solvent with no self energies/forces removed. For the second calculation, this is the force (kJ/mol/A) on the given atom in vacuum with no self energies/forces removed. In other words, these number are basically useless by themselves; their difference gives the total solvation force on the specified atom.
"Fixed charge force on atom ..."
For the first calculation, this is the charge-field force (kJ/mol/A) on the given atom in solvent with no self energies/forces removed. For the second calculation, this is the charge-field force (kJ/mol/A) on the given atom in vacuum with no self energies/forces removed. In other words, these number are basically useless by themselves; their difference gives the reaction field solvation force on the specified atom.
"Ionic boundary force on atom..."
For the first calculation, this would be the ionic boundary force (kJ/mol/A) on the given atom in the solvent if the ionic strength weren't set to zero. For the second calculation, this is identically zero (or very small).
"Dielectric boundary force on atom ..."
For the first calculation, this is the dielectric boundary force (kJ/mol/A) on the given atom in solvent. For the second calculation, this is identically zero (or very small).
"Apolar boundary force on atom ..."
For the first calculation, this is the apolar (surface area dependent) boundary force (kJ/mol/A) on the given atom in solvent. For the second calculation, this is identically zero (or very small).
"Global fixed charge force on atom ..."
This is the reaction field force (kJ/mol/A) on the specified atom.
"Global ionic boundary force on atom ..."
This would be the ionic boundary force (kJ/mol/A) on the specified atom if the ionic strength weren't set to zero.
"Global dielectric boundary force on atom ..."
This is the dielectric boundary force (kJ/mol/A) on the specified atom.
"Global apolar boundary force on atom ..."
This is the apolar boundary force (kJ/mol/A) on the specified atom.

And here's the notation we'll use for the results you should observe (all values in kJ/mol/A):

Solv (runme)
Solvation energy (kJ/mol) from this calculation
Solv (Roux)
Solvation energy from the Roux paper (see above); this was visually approximated from a graph and therefore probably not very close to what they actually obtained
RF (runme)
Reaction field force from this calculation
RF (Roux)
Reaction field force from the Roux paper (see above); this was visually approximated from a graph and therefore probably not very close to what they actually obtained
DB (runme)
Dielectric boundary force from this calculation
DB (Roux)
Dielectric boundary force from the Roux paper (see above); this was visually approximated from a graph and therefore probably not very close to what they actually obtained
IB (runme)
Ionic boundary force from this calculation
IB (Roux)
Ionic boundary force from the Roux paper (see above); this was visually approximated from a graph and therefore probably not very close to what they actually obtained
NP (runme)
Apolar boundary force from this calculation
NP (Roux)
Apolar boundary force from the Roux paper (see above); this was visually approximated from a graph and therefore probably not very close to what they actually obtained
Mol 1 location Solv (runme) Solv (Roux) RF (runme) RF (Roux) DB (runme) DB (Roux) IB (runme) IB (Roux) NP (runme) NP (Roux)
Complex Complex Mol 0Mol 1 Mol 0Mol 1 Mol 0Mol 1 Mol 0Mol 1 Mol 0Mol 1 Mol 0Mol 1 Mol 0Mol 1 Mol 0Mol 1
-3.00 -1.4941E+03 2.0671E-012.0671E-01 0.0E+000.0E+00 -9.7575E-01-9.7575E-01 0.0E+000.0E+00 00 00 -1.6567E-05-1.6567E-05
-2.50 -1.4529E+03 1.0947E+01-1.2476E+01 8.4E+00-1.3E+01 1.1390E+02-1.0268E+02 1.1E+02-1.1E+02 00 00 7.4737E-03-7.4737E-03
-2.00 -1.3952E+03 3.7894E+01-3.6310E+01 3.8E+01-3.4E+01 7.7637E+01-7.7547E+01 8.2E+01-8.2E+01 00 00 8.4697E-03-8.4820E-03
-1.50 -1.3430E+03 6.4344E+01-5.7731E+01 6.3E+01-5.5E+01 4.2190E+01-4.0318E+01 4.2E+01-4.0E+01 00 00 8.6427E-03-8.6407E-03
-1.00 -1.2974E+03 8.6638E+01-8.6808E+01 8.8E+01-8.8E+01 5.6696E+00-2.8578E+00 4.2E+00-4.2E+01 00 00 8.6513E-03-8.6730E-03
-0.50 -1.2539E+03 1.0053E+02-1.0125E+02 1.0E+02-1.0E+02 -1.1362E+012.2136E+01 -1.2E+011.6E+01 00 00 8.7176E-03-8.5418E-03
0.00 -1.2121E+03 1.0591E+020.0000E+00 1.1E+020 -2.1509E+012.9697E+01 -2.1E+012.1E+01 00 00 8.8014E-03-8.3047E-03
0.50 -1.1699E+03 1.0066E+02-1.0172E+02 9.6E+01-9.8E+01 -1.0538E+014.8631E+00 -1.1E+014.2E+00 00 00 7.9753E-03-8.6683E-03
1.00 -1.1255E+03 8.2252E+01-8.7276E+01 8.4E+01-8.8E+01 6.2949E+002.9928E+00 4.2E+000.0E+00 00 00 4.7313E-03-7.9707E-03
1.50 -1.0876E+03 6.5317E+01-6.4707E+01 6.7E+01-6.5E+01 7.2732E+003.1037E+00 6.3E+004.2E+00 00 00 1.8437E-04-6.6104E-04
2.00 -1.0570E+03 5.3014E+01-5.4596E+01 5.3E+01-5.3E+01 7.2734E+001.8664E+00 6.3E+016.3E+01 00 00 -1.1215E-053.8423E-06
2.50 -1.0322E+03 -1.0333E+03 4.3782E+01-4.6578E+01 4.6E+01-4.8E+01 7.2276E+00-2.3296E+00 6.3E+01-2.1E+01 00 00 -1.1215E-05-1.0599E-05
3.00 -1.0114E+03 -1.0128E+03 3.6786E+01-3.6786E+01 3.8E+01-3.8E+01 7.1825E+00-7.1824E+00 6.3E+00-6.3E+00 00 00 -1.1215E-051.12145E-05