L-MOLKERN: a Simulation Package for Polarizable Free-Energy Calculations
Fomin E.S., Alemasov N.A.
Institute of Cytology and Genetics, SB RAS, Novosibirsk 630090, Russia
Abstract. The L-MOLKERN package is proposed to calculate the free-energy differences by λ-dynamics method. To improve the accuracy of calculations of molecules with different charge states the L-MOLKERN uses the new Net-q method for incorporating polarizability. Applications to model systems such as barnase mutants confirm the increase in accuracy. High level of L-MOLKERN scalability for parallel calculations is demonstrated.
Key words: molecular dynamics, λ-dynamics, free-energy differences, polarization, scalability of calculations.