SODIUM is a software that organizes ions around biological macromolecules.
If you're looking for a program that can help you place the required number of sodium ions around a system of electric charges, this is the perfect software for you. One of the best things about this program is that it can easily place ions in the nodes of a cubic grid, where the electrostatic energy is at its lowest.
To achieve this, the program re-computes the energy after the placement of each ion. The energy is computed using a simple Coulombic formula, which basically involves summing all the Q_i values and dividing them by the difference between two points. While some users may not like the weird energy units that this formula generates, this doesn't really matter when it comes to energy comparison.
To speed things up, the atoms of the macromolecule can be relocated to the grid nodes that are closest to their original locations. This results in minimal errors, when compared to placing ions one-by-one or using simplified energy functions.
If you do decide to use this program, you'll find that it also prints out the coordinates of the placed ions in the PDB format. This makes it easy for you to use the ions for further purposes.
However, it's important to note that this program doesn't take into account the equilibration of placed ions. For best results, it's recommended that you run a separate Monte Carlo or Molecular Dynamics simulation to equilibrate the ions before further usage.
One of the best things about this program is that it can be easily modified to allow the placement of any combination of multivalent ions of different charges. This makes it an incredibly versatile tool for anyone who is working with electric charges or macromolecules.
To achieve this, the program re-computes the energy after the placement of each ion. The energy is computed using a simple Coulombic formula, which basically involves summing all the Q_i values and dividing them by the difference between two points. While some users may not like the weird energy units that this formula generates, this doesn't really matter when it comes to energy comparison.
To speed things up, the atoms of the macromolecule can be relocated to the grid nodes that are closest to their original locations. This results in minimal errors, when compared to placing ions one-by-one or using simplified energy functions.
If you do decide to use this program, you'll find that it also prints out the coordinates of the placed ions in the PDB format. This makes it easy for you to use the ions for further purposes.
However, it's important to note that this program doesn't take into account the equilibration of placed ions. For best results, it's recommended that you run a separate Monte Carlo or Molecular Dynamics simulation to equilibrate the ions before further usage.
One of the best things about this program is that it can be easily modified to allow the placement of any combination of multivalent ions of different charges. This makes it an incredibly versatile tool for anyone who is working with electric charges or macromolecules.
What's New
Version 1.5.1: N/A