APBS

From Henkelman Group

Experimental parameters:

1. F8BT Nanoparticle

  dielectric constant= 3
  There are ~10,000 monomers (radius~7A) in one nanoparticle with a radius of 15nm.
  One nanoparticle could contain ~1000 holes.
  It's unknown that how many monomers compose of one oxidizable site that could have +1e charge. 
  

2. Electrolyte solution: 0.1M LiClO4 in Acetonitrile

  cation: +1e, 0.1M, radius= 0.60A
  anion: -1e, 0.1M, radius= 2.36A
  solvent molecule radius= 2.24A, dielectric constant= 37.5

This is where the grid spacing is mentioned, hx,hy,hz <0.5 for good results.

• Error control:

etol{tol} is the variable to set the tolerance for the grid refinement. ekey{flag} should be set prior, where {flag} = simpl, global or frac. simpl means the tolerance applies to each simplex, global sets the total error, frac sets the fraction of simplices to be refined...

[general APBS stuff]

Simple input for a .pqr file that defines a single ion with specific radius.

 REMARK Ion with 2.00 A radius and +1 e chareg
 ATOM      1  I   ION     1       0.000   0.000   0.000  1.00  2.00

APBS tutorial at sourceforge. There are some suggestions for visualizing things that may be helpful. Note also that at least with my (brad's) APBS install I have to add "gamma 0.14" to both the solv and ref param lists of the sample input file. The value 0.14 is completely arbitrary but has to do with surface tension (if I remember correctly). I also think the definitions for the grid dimension and spacing make a lot more sense in this input file.

This input file will read the above pqr (named ion.pqr) and write the potential in a dx file. The solvation energy is also calculated...

APBS input file

I managed to find a python script that cuts the relevant info from the dx file. It's pasted at:
Potential Extraction dot py
Just ignore the fact that the wiki puts boxes around everything. You should be able to cut and paste the script and the boxes get ignored. If you are on a machine with python, type 'python potential_extraction.py potential.dx> output' and provided you saved the script as potential_extraction.py, you should get a file named 'output' that has the potential as a function of distance from the ion.

If you installed APBS, you might find this script in /usr/shar/doc/apbs/html/tutorial/examples/born/born.tar.gz... read the bash script there to sort out what's going on.

Here is a plot of the potential for a 3 angstrom and 10 angstrom particle:

If you zoom in you can see the potential is the same on the outside of the particles but very different inside them: