The inconsistency in MD simulation regarding 1-4 interactions
The problem of conflicting factors In MD simulation, in amber force field using 0.5 and 0.8333 scaling factors for 1-4 interaction van der waals and columbic interactions. However, in glycam based force field, these two scaling factors are set as 1.0 both. In case we need to simulate a protein using amber force field and the LPS lipid using the glycam based force field in Gromacs, then there comes the problem. Because in Gromacs, the setting for these two factors (fugeJJ and fugeQQ) is written in the "[default]" field for the whole simulation system. Therefore, in order to generate 1-4 interactions for protein and LPS molecules, it will be incompatible. How to solve the problem? 1. Change protein force field to OPLS, using OPLS force field for LPS as well. Or choosing other force field. 2. Manually define the 1-4 interactions. But sadly only for vdw interactions. We could explicitly add parameters for 1-4 LJ interactions in the "pair" field.