FREE ENERGY CALCULATION FOR GRAMICIDIN A (GA) CHANNEL WITH NO EQUILIBRIUM REQUIREMENT

Yıl 2016, Cilt: 12 Sayı: 2, 14 - 14, 01.08.2016

Murat Çavuş Murat Şahan Turgut Baştuğ

Öz

Today, the most important reason of the work with molecular dynamics simulation method
of biomolecular systems is to ensure understanding physical mechanism and dynamic properties that
is not readily accessible to experimental methods. Gramicidin channels (Figure 1) are bacterial
channels with radius of approximately 2 Å. The channel is a simple test system for controlling the
accuracy of the method of free energy and force field because of the simple structure. In addition,
theoretical calculations of free energy that called Crooks fluctuation theorem for non-equilibrium
systems are available at literature. In this study, primarily, free energy calculation methods that do
not require equilibrium state were developed for complex systems and compared with the free energy
simulation work in equilibrium condition. Finally the validity of the method was tested for the GA
channels.

Anahtar Kelimeler

Gramicidin A Channel, Crooks Fluctuation Theorem, Non-equilibrium Systems