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Mat. Biolog. Bioinform., 2012, Volume 7, Issue 2, Pages 398–409 (Mi mbb112)  

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.

Full text: PDF file (379 kB)
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UDC: 004.94
Received 16.07.2012, Published 26.07.2012

Citation: Eduard S. Fomin, Nikolay A. Alemasov, “L-MOLKERN: a Simulation Package for Polarizable Free-Energy Calculations”, Mat. Biolog. Bioinform., 7:2 (2012), 398–409

Citation in format AMSBIB
\Bibitem{FomAle12}
\by Eduard~S.~Fomin, Nikolay~A.~Alemasov
\paper L-MOLKERN: a~Simulation Package for Polarizable Free-Energy Calculations
\jour Mat. Biolog. Bioinform.
\yr 2012
\vol 7
\issue 2
\pages 398--409
\mathnet{http://mi.mathnet.ru/mbb112}


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