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sodium


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OS: Linux, ...

License: Freeware





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 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.

http://www.ks.uiuc.edu/Development/MDTools/sodium/



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