[HTML][HTML] Magic v. 3: An integrated software package for systematic structure-based coarse-graining

A Mirzoev, L Nordenskiöld, A Lyubartsev - Computer Physics …, 2019 - Elsevier
Molecular simulations of many phenomena related to biomolecular systems, soft matter and
nanomaterials require consideration of length scales above 10 nm and time scales longer …

Systematic coarse graining of biomolecular and soft-matter systems

GS Ayton, WG Noid, GA Voth - Mrs Bulletin, 2007 - Springer
Coarse-grained modeling is a key component in the field of multiscale simulation. Many
biomolecular and otherwise complex systems require the characterization of phenomena …

[HTML][HTML] Introduction: Coarse-graining in molecular modeling and simulation

GA Voth - Journal of Chemical Theory and Computation, 2006 - ACS Publications
This partial special issue of the Journal of Chemical Theory and Computation is devoted to
the topic of coarsegraining in molecular modeling and simulation. To my knowledge, it is the …

Neural network based prediction of conformational free energies-a new route toward coarse-grained simulation models

T Lemke, C Peter - Journal of chemical theory and computation, 2017 - ACS Publications
Coarse-grained (CG) simulation models have become very popular tools to study complex
molecular systems with great computational efficiency on length and time scales that are …

MagiC: Software package for multiscale modeling

A Mirzoev, AP Lyubartsev - Journal of chemical theory and …, 2013 - ACS Publications
We present software package MagiC, which is designed to perform systematic structure-
based coarse graining of molecular models. The effective pairwise potentials between …

[HTML][HTML] A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

S Markutsya, MH Lamm - The Journal of Chemical Physics, 2014 - pubs.aip.org
We report on a new approach for deriving coarse-grained intermolecular forces that retains
the frictional contribution that is often discarded by conventional coarse-graining methods …

Coarse-grained modeling of simple molecules at different resolutions in the absence of good sampling

L Larini, JE Shea - The Journal of Physical Chemistry B, 2012 - ACS Publications
Many problems of interest in modern science originate from the complex network of
interactions of different molecular structures, each possessing its own typical length and time …

The Multiscale Coarse-Graining Method: A Systematic Approach to Coarse Graining

WG Noid, GS Ayton, S Izvekov… - Coarse-graining of …, 2009 - books.google.com
Atomistic molecular dynamics (MD) simulations [Allen and Tildesley 1987; Frenkel and Smit
2002] remain one of the most powerful tools for computationally modeling biomolecular and …

On developing coarse-grained models for biomolecular simulation: a review

S Riniker, JR Allison, WF van Gunsteren - … Chemistry Chemical Physics, 2012 - pubs.rsc.org
So-called coarse-grained models are a popular type of model for accessing long time scales
in simulations of biomolecular processes. Such models are coarse-grained with respect to …

25 Structure-Based Coarse-and Fine-Graining in Soft Matter Simulations

NFA van der Vegt, C Peter… - Coarse-graining of …, 2008 - books.google.com
Many physical phenomena in biology, chemistry, and materials science involve processes
occurring on atomistic length and time scales, which affect structural and dynamical …