Approach to Thermal Equilibrium in Biomolecular Simulation
نویسندگان
چکیده
The evaluation of molecular dynamics models incorporating temperature control methods is of great importance for molecular dynamics practitioners. In this paper, we study the way in which biomolecular systems achieve thermal equilibrium. In unthermostatted (constant energy) and Nosé-Hoover dynamics simulations, correct partition of energy is not observed on a typical MD simulation timescale. We discuss the practical use of numerical schemes based on Nosé-Hoover chains, Nosé-Poincaré and recursive multiple thermostats (RMT) [8], with particular reference to parameter selection, and show that RMT appears to show the most promise as a method for correct thermostatting. All of the MD simulations were carried out using a variation 2 of the CHARMM package in which the Nosé-Poincaré, Nosé-Hoover Chains and RMT methods have been implemented.
منابع مشابه
Effect of Biomolecular Conformation on Docking Simulation: A Case Study on a Potent HIV-1 Protease Inhibitor
Human immunodeficiency virus infection / acquired immunodeficiency syndrome (HIV/AIDS) is a disease pertained to the human immune system. Given its crucial role in viral replication, HIV-1 protease (HIV-1 PR) is a prime therapeutic target in AIDS therapy. In this regard, the dynamic aspects of ligand-enzyme interactions may indicate an important role of conformational variability in HIV-1 PR in...
متن کاملRole of Interatomic Potentials in Simulation of Thermal Transport in Carbon Nanotubes
Interatomic potentials, which describe interactions between elements of nanosystems, are crucial in theoretical study of their physical properties. We focus on two well known empirical potentials, i.e. Tersoff's and Brenner's potentials, and compare their performance in calculation of thermal transport in carbon nanotubes. In this way, we study the temperature and diameter dependence of thermal...
متن کاملSlip flow in porous micro-tubes under local thermal non-equilibrium conditions
In the present work, forced convection heat transfer of slip flow in porous micro-tubes with local thermal non-equilibrium between the gas and the solid matrix is investigated numerically. For this purpose, the flow is considered hydrodynamically developed but thermally developing. The Darcy-Brinkman-Forchheimer model in conjunction with separate energy equations for the gas and the solid matri...
متن کاملEffect of Biomolecular Conformation on Docking Simulation: A Case Study on a Potent HIV-1 Protease Inhibitor
Human immunodeficiency virus infection / acquired immunodeficiency syndrome (HIV/AIDS) is a disease pertained to the human immune system. Given its crucial role in viral replication, HIV-1 protease (HIV-1 PR) is a prime therapeutic target in AIDS therapy. In this regard, the dynamic aspects of ligand-enzyme interactions may indicate an important role of conformational variability in HIV-1 PR in...
متن کاملDevelopment of simulation model for performance evaluation of feed water system in a typical thermal power plant
The present paper deals with development of a simulation model for the performance evaluation of feed water system of a thermal power plant using Markov Birth-Death process and probabilistic approach. In present paper, the feed water system consists of four subsystems. After drawing transition diagram for feed water system, differential equations are developed and then solved recursively using ...
متن کامل