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Volume 7   Issue 2   Year 2012
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

fomin@bionet.nsc.ru

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.

Table of Contents Original Article
Math. Biol. Bioinf.
2012;7(2):398-409
doi: 10.17537/2012.7.398
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References

 

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