Related Experiment Video
Updated: Dec 20, 2025

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
Published on: September 17, 2021
Numeric analysis of reversibility of classic movement equations and constructive criteria of estimating quality of
Ivan Yu Torshin1, Vladimir A Namiot2, Natalia G Esipova3
1Dorodnicyn Computing Centre, Russian Academy of Sciences, FIC IU RAS, Moscow, Russian Federation.
Abstract:
The fundamental criteria of the quality of molecular dynamics (MD) simulation represent a pivotal challenge, especially in the case of MD simulations of large systems (in particular, proteins).This work presents a simple theoretical analysis of time reversibility in classical mechanics that has allowed us to formulate a number of constructive criteria for evaluating the quality of the trajectories, generated in MD simulations. The results of testing the criteria on the structures of eight small proteins are presented. The criteria can be useful for solving different MD problems, such as: choosing the most appropriate thermostats for a MD system under study, the methods for sampling conformations, etc.Communicated by Ramaswamy H. Sarma.
More Related Videos
11:03An Analog Macroscopic Technique for Studying Molecular Hydrodynamic Processes in Dense Gases and Liquids
Published on: December 4, 2017
09:17Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
Published on: March 1, 2022
Related Concept Videos
Chemical Reactions
The relative amounts of reactants and products represented in a balanced chemical equation are often referred to as stoichiometric amounts. However, in...
Woodward–Hoffmann Selection Rules and Microscopic Reversibility
Dynamic Equilibrium
Stability of Equilibrium Configuration
A stable equilibrium occurs when a system tends to return to its original position when given a small displacement, and the potential energy is at its minimum. An example of a stable equilibrium is when a cantilever beam is fixed at one end and a weight is attached to the other end. If the weight...
Reaction Quotient
Linear Approximation in Time Domain
For a simple pendulum with a mass evenly distributed along its length and the center of mass located at half the pendulum's length,...