Abstract
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.
Details
| Other ID | JA78RJ59SS |
|---|---|
| Journal Section | Articles |
| Authors | |
| Publication Date | August 1, 2016 |
| Submission Date | August 1, 2016 |
| Published in Issue | Year 2016 Volume: 12 Issue: 2 |