Robosample: A rigid-body molecular simulation program based on robot mechanics

• Published in: Biochimica et biophysica acta. General subjects Vol. 1864; no. 8; p. 129616
• Main Authors: Spiridon, Laurentiu, Şulea, Teodor Asvadur, Minh, David D.L., Petrescu, Andrei-Jose
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.08.2020
• Subjects: alanine; Alanine - chemistry; algorithms; computer simulation; computer software; dipeptides; Dipeptides - chemistry; Gibbs free energy; Gibbs sampling; Hamiltonian Monte Carlo; mechanical engineering; mechanics; Molecular dynamics; Molecular Dynamics Simulation; Monte Carlo Method; Multibody dynamics; Robotics; robots; Software; Molecular dynamics; Multibody dynamics; Hamiltonian Monte Carlo; Gibbs sampling; Robotics

Compared with all-atom molecular dynamics (MD), constrained MD methods allow for larger time steps, potentially reducing computational cost. For this reason, there has been continued interest in improving constrained MD algorithms to increase configuration space sampling in molecular simulations. He...