Polarizable force field
The potential function is one of the most important ingredients in MD calculations. Many of the current simulations of biomolecular systems are based on a potential function representing the interactions between non-bonded atoms in terms of a Lennard-Jones 6-12 potential and fixed atomic partial charge coulomb electrostatics. In our group we normally use the potential function of the CHARMM biomolecular simulation program. Other similar potential functions are AMBER , and GROMOS . We think that such simple models, which ignore electronic polarization effects, will be insufficient for understanding the microscopic basis of ion selectivity in biological channels. We are currently developing a force field which will include induced polarization (see Lamoureux et al, 2003, Lamoureux et al, 2005, Harder et al, 2009).