CHARMM Development Project Forums User Discussion & Questions Energy terms, Constraints, Restraints, and Solvation add ions at a structure

Hello everyone,


I want to perform a simulation at a concentration of 0.15 M. However, my pdb structure already has some, and these ions are placed strategically, I cannot change their position.

How not to destroy the position of the ions already present and to add some for an optimal concentration.


Best,
Johan

That depends on the software packages being used, the force field, and the bound ion types.

The charmm-gui site may offer an easy path to this, assuming the PDB file ion types are all in the CHARMM force field.

Any water molecules in the PDB file may also be important to retain.