Related Experiment Video
Updated: Mar 9, 2026

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
Published on: September 17, 2021
Introduction of steered molecular dynamics into UNRES coarse-grained simulations package
Adam K Sieradzan1, Rafał Jakubowski2
1Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, 80-308, Poland.
Abstract:
In this article, an implementation of steered molecular dynamics (SMD) in coarse-grain UNited RESidue (UNRES) simulations package is presented. Two variants of SMD have been implemented: with a constant force and a constant velocity. The huge advantage of SMD implementation in the UNRES force field is that it allows to pull with the speed significantly lower than the accessible pulling speed in simulations with all-atom representation of a system, with respect to a reasonable computational time. Therefore, obtaining pulling speed closer to those which appear in the atomic force spectroscopy is possible. The newly implemented method has been tested for behavior in a microcanonical run to verify the influence of introduction of artificial constrains on keeping total energy of the system. Moreover, as time dependent artificial force was introduced, the thermostat behavior was tested. The new method was also tested via unfolding of the Fn3 domain of human contactin 1 protein and the I27 titin domain. Obtained results were compared with Gø-like force field, all-atom force field, and experimental results. © 2017 Wiley Periodicals, Inc.
More Related Videos
05:00Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
Published on: August 9, 2024
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
Molecular Models
Molecular Weight of Step-Growth Polymers
As the step-growth polymerization involves step-wise condensation of monomers, the molecular weight also builds up eventually. Consequently, high molecular weight polymers are obtained at the late stages of the polymerization, where 99% of monomers have been consumed.
The extent of the...
Step-Growth Polymerization: Overview
Many natural and synthetic polymers are produced by...
Distribution of Molecular Speeds
An Introduction to Mechanics
According to records, the history of mechanics starts with Aristotle (384–322 BC). He related mechanics to physical theory, aiming for a universal synthesis.
Newton defined mechanics as the branch of physical science that...
Three-Dimensional Force System