2025/08/28 by Luis Vollmers, Shuyu Chen, Maria Reif +2 · 1 voice
Chemistry · Physics and Astronomy · #Advanced Physical and Chemical Molecular Interactions #Advanced Thermodynamics and Statistical Mechanics #Computer science #Data science #Dynamics (music) #Sociology #Various Chemistry Research Topics
paper · doi:10.33011/livecoms.6.1.3797
published in Living Journal of Computational Molecular Science 6(1), 3797 (University of Colorado Boulder)
openalex publication_date 2025/08/28 · openalex created_date 2025/10/10 · openalex updated_date 2026/06/11
This tutorial equips natural scientists with the essential knowledge needed to utilize and comprehend molecular dynamics simulations effectively. Beginning with the stability of integration algorithms and the conservation of energy, this article proceeds with the description of atomistic forcefields, thermodynamic ensembles, long-range electrostatics treatment, and free energy calculations within molecular dynamics simulations. It then extends to the simulation of proteins and drug discovery applications. This comprehensive overview includes numerous references to relevant publications and tackles real-world problems. The tutorial is based on a 10-week master’s course typically undertaken by students in the first or second semester of their master’s program.