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Introduction
This program places the required number of sodium ions around a system
of electric charges, e.g., the atoms of a biological macromolecule (protein,
DNA, protein/DNA complex). The ions are placed in the nodes of a cubic grid,
in which the electrostatic energy achieves the smallest values. The energy
is re-computed after placement of each ion. A simple Coulombic formula
is used for the energy:
Energy(R) = Sum(i_atoms,ions) Q_i / |R-R_i|
All the constants are dropped out from this formula, resulting in some
weird energy units; that doesn't matter for the purpose of energy comparison.
To speed the program up, the atoms of the macromolecule are re-located to
the grid nodes, closest to their original locations. The resulting error
is believed to be minor, compared to that resulting from the one-by-one
ions placement, or from using the simplified energy function.
The coordinates of the placed ions are printed out in the PDB format for
further usage. It is recommended that the placed ions are equilibrated in
a separate Monte Carlo or Molecular Dynamics simulation.
Trivial modifications to the program should allow the placement of any
combination of multivalent ions of different charges.
Contact
If you have questions please send email to the author Alexander Balaeff,
at sure@ks.uiuc.edu
Download
License
Same terms as NAMD license
Documentation
Please see the sodium.c source code header for usage information
and platform-specific comments.
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