Dear all,
I originally thought that the charge of an atom was determined by the type of atom in a given force field. But I checked the pcff force field file in EMC and found no code about charge assignment. May I ask how the pcff force field assigns the atomic charge in EMC?
Hi Starry,
With the PCFF force field, the charge assignment comes through a bond increment system. Some atoms types have an initial charge assigned to them directly (i.e. an [Na+] ion atom would initially be given a charge of +1) but for most of them it is done through a bond increment system. This means that when you have a bond between two atoms i and j, there is a partial charge that is added to atom i and equivalently subtracted off of atom j to keep electroneutrality in the system. This is in the “Bond Increments” section of “pcff.frc”.
From what I understand these are initially derived from ab-initio quantum mechanical calculations, but some literature will replace these charges with their own partial charges calculated from a restrained electrostatic potential (RESP) fitting or some other method. I haven’t explored this yet personally but you’d need another program like Gaussian or something to do that.
Sam
Dear user,
Sam indeed is correct. PCFF – and also a number of other force fields in EMC – uses bond increments to assign partial charges. As the name implies, partial charges are a sum of increments as provided by each bond. Typically, most force fields abide by these rules. For instance, the version of CHARMM as provided by EMC is based on this observation and also uses the concept of bond increments as opposed to direct charge assignment. OPLS in EMC is one of the few force fields, that use the latter rather than the former. Bond increments make a force field far more flexible. The reason that OPLS does not include bond increments is due to the fact, that I don’t use the force field much myself. That is not to say, that the machinery under the hood of EMC would not support bond increments for OPLS. One would have to redefine the force field parameter and rule files though.
Dear Sam and Veld,
Thank you very much for your detailed explanations, very helpful! I understand now.