L-MOLKERN: a Simulation Package for Polarizable Free-Energy Calculations

The L-MOLKERN package is proposed to calculate the free-energy differences by $\lambda$-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.