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 0 | Mol 1 |
Mol 0 | Mol 1 |
Mol 0 | Mol 1 |
Mol 0 | Mol 1 |
Mol 0 | Mol 1 |
Mol 0 | Mol 1 |
Mol 0 | Mol 1 |
Mol 0 | Mol 1 |
-3.00 |
-1.4941E+03 |
|
2.0671E-01 | 2.0671E-01 |
0.0E+00 | 0.0E+00 |
-9.7575E-01 | -9.7575E-01 |
0.0E+00 | 0.0E+00 |
0 | 0 |
0 | 0 |
-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 |
0 | 0 |
0 | 0 |
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 |
0 | 0 |
0 | 0 |
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 |
0 | 0 |
0 | 0 |
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 |
0 | 0 |
0 | 0 |
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+01 | 2.2136E+01 |
-1.2E+01 | 1.6E+01 |
0 | 0 |
0 | 0 |
8.7176E-03 | -8.5418E-03 |
| |
0.00 |
-1.2121E+03 |
|
1.0591E+02 | 0.0000E+00 |
1.1E+02 | 0 |
-2.1509E+01 | 2.9697E+01 |
-2.1E+01 | 2.1E+01 |
0 | 0 |
0 | 0 |
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+01 | 4.8631E+00 |
-1.1E+01 | 4.2E+00 |
0 | 0 |
0 | 0 |
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+00 | 2.9928E+00 |
4.2E+00 | 0.0E+00 |
0 | 0 |
0 | 0 |
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+00 | 3.1037E+00 |
6.3E+00 | 4.2E+00 |
0 | 0 |
0 | 0 |
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+00 | 1.8664E+00 |
6.3E+01 | 6.3E+01 |
0 | 0 |
0 | 0 |
-1.1215E-05 | 3.8423E-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 |
0 | 0 |
0 | 0 |
-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 |
0 | 0 |
0 | 0 |
-1.1215E-05 | 1.12145E-05 |
| |