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

Eduard S. Fomin ; Nikolay A. Alemasov

Matematičeskaâ biologiâ i bioinformatika, Tome 7 (2012) no. 2, pp. 398-409.

Résumé

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.

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