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Free energy calculations of alanine tripeptide in explicit water using temperature accelerated sliced sampling

Authors : Anji Babu Kapakayala, Abhinav Gupta, Shivani Verma and Nisanth N. Nair



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Abstract

Enhanced sampling of high dimensional free energy surfaces through molecular dynamics (MD) methods is crucial for its application in studying complex chemical reactions and conformational changes in condensed matter. Recently, we have introduced a technique called Temperature Accelerated Sliced Sampling (TASS) (J. Chem. Phys., 2017, 146, 94108) for computing high dimensional free energy surfaces in a computationally efficient manner. In this article, we demonstrate the application of this method in calculating free energy surface as a function of Ramachandran angles of alanine tripeptide in explicit water. We show that the method out-performs other conventional sampling methods like metadynamics and temperature accelerated molecular dynamics/driven-adiabatic free energy dynamics. Further, we discuss the differences between free energy surfaces in vacuo and in solution, and characterize different conformational states. The results of this work is of great importance as alanine tripeptide in solution is an ideal benchmark system for the methods to sample high dimensional free energy landscapes.

 

Keyword

Free energy calculations, enhanced sampling methods, alanine tripeptide, temperature-accelerated sliced sampling, molecular dynamics