Bioinformatics

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

Eduard S. Fomin, Nikolay A. Alemasov

Institute of Cytology and Genetics, SB RAS, Novosibirsk 630090, Russia

Abstract: 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.

Key words: molecular dynamics, $\lambda$-dynamics, free-energy differences, polarization, scalability of calculations.

UDC: 004.94

Received 16.07.2012, Published 26.07.2012