Description of Neutralization

Some structures may not be neutral but instead have a positive or negative net charge. Some methods in CHARMM, such as the Ewald method for computing electrostatics, fail when there is net charge on the system so it is best to neutralize the charge by adding counter ions to the solution. When CHARMM reads in or modifies a PSF, it will output the total charge of the system as shown in the following sample output.

The charge can also be calculated by printing out the ?STOT variable after running the "SCALar CHARge STAT" command.

However, adding charged particles close to a protein may influence its behavior. is undesirable, and therefore care must be taken to place ions far away where they will be screened by solvent.