Two decades of Martini: Better beads, broader scope

SJ Marrink, L Monticelli, MN Melo… - Wiley …, 2023 - Wiley Online Library
The Martini model, a coarse‐grained force field for molecular dynamics simulations, has
been around for nearly two decades. Originally developed for lipid‐based systems by the …

Perspective: Coarse-grained models for biomolecular systems

WG Noid - The Journal of chemical physics, 2013 - pubs.aip.org
By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …

The MARTINI force field: coarse grained model for biomolecular simulations

SJ Marrink, HJ Risselada, S Yefimov… - The journal of …, 2007 - ACS Publications
We present an improved and extended version of our coarse grained lipid model. The new
version, coined the MARTINI force field, is parametrized in a systematic way, based on the …

The MARTINI coarse-grained force field: extension to proteins

L Monticelli, SK Kandasamy, X Periole… - Journal of chemical …, 2008 - ACS Publications
Many biologically interesting phenomena occur on a time scale that is too long to be studied
by atomistic simulations. These phenomena include the dynamics of large proteins and self …

Coarse grained model for semiquantitative lipid simulations

SJ Marrink, AH De Vries, AE Mark - The Journal of Physical …, 2004 - ACS Publications
This paper describes the parametrization of a new coarse grained (CG) model for lipid and
surfactant systems. Reduction of the number of degrees of freedom together with the use of …

A review of advancements in coarse-grained molecular dynamics simulations

SY Joshi, SA Deshmukh - Molecular Simulation, 2021 - Taylor & Francis
Over the last few years, coarse-grained molecular dynamics has emerged as a way to model
large and complex systems in an efficient and inexpensive manner due to its lowered …

A multiscale coarse-graining method for biomolecular systems

S Izvekov, GA Voth - The Journal of Physical Chemistry B, 2005 - ACS Publications
A new approach is presented for obtaining coarse-grained (CG) force fields from fully
atomistic molecular dynamics (MD) trajectories. The method is demonstrated by applying it …

Water in nanopores and biological channels: a molecular simulation perspective

CI Lynch, S Rao, MSP Sansom - Chemical reviews, 2020 - ACS Publications
This Review explores the dynamic behavior of water within nanopores and biological
channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside …

The power of coarse graining in biomolecular simulations

HI Ingólfsson, CA Lopez, JJ Uusitalo… - Wiley …, 2014 - Wiley Online Library
Computational modeling of biological systems is challenging because of the multitude of
spatial and temporal scales involved. Replacing atomistic detail with lower resolution …

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

WG Noid, JW Chu, GS Ayton, V Krishna… - The Journal of …, 2008 - pubs.aip.org
Coarse-grained (CG) models provide a computationally efficient method for rapidly
investigating the long time-and length-scale processes that play a critical role in many …