POTENTIAL-ENERGY FUNCTION AND PARAMETERS FOR SIMULATIONS OF THE MOLECULAR-DYNAMICS OF PROTEINS AND NUCLEIC-ACIDS IN SOLUTION

We present the complete set of energy parameters used in the ENCAD (Energy Calculation and Dynamics) simulation program [J. Mol. Biol. 168 (1983) 595]. Full details are given of the form of the potential, which has been designed for efficient simulation of trajectories of macromolecules in solution. Emphasis is placed on energy conservation and the nonbonded truncation schemes needed to achieve it. Simulations of macromolecules in solution with ENCAD are both very stable in that the native structure is preserved at room temperature and efficient in that nanosecond simulations take a few weeks on an ordinary workstation.