The CHARMM force field is one of the most widely used atomistic force fields in biomolecular simulation. Currently, the force field covers proteins, nucleic acids, lipids, carbohydrates, ions, small molecules, and a wide range of modified (noncanonical) residues within each of these categories. Augmenting the core CHARMM force field is the CHARMM General Force Field (CGenFF), which can be applied to nonstandard species, most often ligands and drug-like molecules. In this webinar, the functional form and parametrization strategy of the CHARMM force field will be presented along with key features that can be exploited for simulations of complex systems. Other topics include the implementation of the force field in the GROMACS simulation software and details on how users can convert CGenFF-generated topologies into GROMACS format for use in simulations.
Justin Lemkul earned his PhD in Biochemistry under the supervision of Prof. David R. Bevan in the Department of Biochemistry at Virginia Tech. His dissertation work focused on conformational dynamics of the amyloid b-peptide in membrane environments and the interactions of this protein with small molecules. He received a Ruth L. Kirschstein fellowship from the National Institutes of Health for his postdoctoral work with Prof. Alexander D. MacKerell, Jr. at the University of Maryland, Baltimore, where he contributed to the development of the Drude polarizable force field for nucleic acids. Since 2017, he has been an Assistant Professor in the Department of Biochemistry at Virginia Tech, where his group has focused on polarizable simulations of amyloidogenic proteins and DNA and RNA G-quadruplexes.