scholarly journals Calculation of Local Water Densities in Biological Systems: A Comparison of Molecular Dynamics Simulations and the 3D-RISM-KH Molecular Theory of Solvation

2011 ◽  
Vol 115 (2) ◽  
pp. 319-328 ◽  
Author(s):  
Martin C. Stumpe ◽  
Nikolay Blinov ◽  
David Wishart ◽  
Andriy Kovalenko ◽  
Vijay S. Pande
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Biological Systems ◽  
Molecular Theory ◽  
Local Water ◽  
Dynamics Simulations

scholarly journals Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications

2019 ◽  
Vol 20 (15) ◽  
pp. 3774 ◽  
Author(s):  
Nidhi Singh ◽  
Wenjin Li
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
Structure Prediction ◽  
Biological Systems ◽  
Conformational Dynamics ◽  
Multiscale Simulation ◽  
Coarse Grained ◽  
Hierarchical Level ◽  
Dynamics Simulations

Molecular dynamics simulations have emerged as a powerful tool to study biological systems at varied length and timescales. The conventional all-atom molecular dynamics simulations are being used by the wider scientific community in routine to capture the conformational dynamics and local motions. In addition, recent developments in coarse-grained models have opened the way to study the macromolecular complexes for time scales up to milliseconds. In this review, we have discussed the principle, applicability and recent development in coarse-grained models for biological systems. The potential of coarse-grained simulation has been reviewed through state-of-the-art examples of protein folding and structure prediction, self-assembly of complexes, membrane systems and carbohydrates fiber models. The multiscale simulation approaches have also been discussed in the context of their emerging role in unravelling hierarchical level information of biosystems. We conclude this review with the future scope of coarse-grained simulations as a constantly evolving tool to capture the dynamics of biosystems.

Investigating biological systems using first principles Car–Parrinello molecular dynamics simulations

2007 ◽  
Vol 17 (2) ◽  
pp. 149-156 ◽  
Author(s):  
Matteo Dal Peraro ◽  
Paolo Ruggerone ◽  
Simone Raugei ◽  
Francesco Luigi Gervasio ◽  
Paolo Carloni
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
First Principles ◽  
Biological Systems ◽  
Dynamics Simulations
Sign in / Sign up

Export Citation Format

Share Document