Hi everyone, I have a confusion regarding the charmm36 forcefield. Why are the charges present in the ffnonbonded.itp file are all zero? How can we reliably use charmm36 forcefields for a system with zero charge for any atom? Is there any other way they define the charges in charmm36 forcefield? Any help will be much appreciated
Charges are never read from ffnonbonded.itp by any force field. The residue definitions in the relevant .rtp files are used.
Thank you for your reply Dr. Lemkul. In other forcefields such as: OPLS-AA, in the ffnonbonded.itp file all non-bonded parameters sigma, epsilon (for LJ) and partial charges for Coulomb interactions are provided. As you mentioned I have checked the cgenff.rtp file and it seems that a particular atomtype partial charge is different for different molecules. For example an atomtype: OG2P1, the partial charge is different for different types of molecules. How does the forcefield determine which value to use? I was of the impression that a particular atomtype will have a particular set of non-bonding parameters and based on that cross-terms will be calculated by gromacs.
Charges are listed in ffnonbonded.itp because long ago there was an intention to implement a general topology builder. This plan was abandoned. The charges in that file have no meaning and there is not a formal association between charge and atom type in any force field, regardless of whether values are present in that file or not.
Charges in the .rtp entry are used. LJ parameters come from ffnonbonded.itp.