4.4 Article

Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

Related references

Note: Only part of the references are listed.
Article Physics, Multidisciplinary

Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations

K. Kreis et al.

EUROPEAN PHYSICAL JOURNAL-SPECIAL TOPICS (2015)

Article Physics, Multidisciplinary

Adaptive resolution simulation in equilibrium and beyond

H. Wang et al.

EUROPEAN PHYSICAL JOURNAL-SPECIAL TOPICS (2015)

Article Chemistry, Physical

Systematic hierarchical coarse-graining with the inverse Monte Carlo method

Alexander P. Lyubartsev et al.

JOURNAL OF CHEMICAL PHYSICS (2015)

Article Chemistry, Physical

Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

Julija Zavadlav et al.

JOURNAL OF CHEMICAL PHYSICS (2015)

Article Chemistry, Physical

Exploring Lacl-DNA Dynamics by Multiscale Simulations Using the SIRAH Force Field

Matias R. Machado et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

Adaptive Resolution Simulation of a DNA Molecule in Salt Solution

Julija Zavadlav et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

Martini Coarse-Grained Force Field: Extension to DNA

Jaakko J. Uusitalo et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations

Tsjerk A. Wassenaar et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field

Yifei Qi et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

Characterization of the Local Structure in Liquid Water by Various Order Parameters

Elise Duboue-Dijon et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2015)

Article Chemistry, Physical

Systematic evaluation of bundled SPC water for biomolecular simulations

Srinivasa M. Gopal et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2015)

Article Chemistry, Physical

Hydrophobicity: effect of density and order on water's rotational slowing down

John Tatini Titantah et al.

SOFT MATTER (2015)

Article Chemistry, Physical

Hydration repulsion between membranes and polar surfaces: Simulation approaches versus continuum theories

Matej Kanduc et al.

ADVANCES IN COLLOID AND INTERFACE SCIENCE (2014)

Review Chemistry, Multidisciplinary

Classical Electrostatics for Biomolecular Simulations

G. Andres Cisneros et al.

CHEMICAL REVIEWS (2014)

Article Biochemistry & Molecular Biology

Theoretical frameworks for multiscale modeling and simulation

Huan-Xiang Zhou

CURRENT OPINION IN STRUCTURAL BIOLOGY (2014)

Article Chemistry, Physical

Coarse-grained modeling of DNA oligomer hybridization: Length, sequence, and salt effects

Daniel M. Hinckley et al.

JOURNAL OF CHEMICAL PHYSICS (2014)

Article Chemistry, Physical

Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond

Piero Gasparotto et al.

JOURNAL OF CHEMICAL PHYSICS (2014)

Article Chemistry, Physical

Adaptive resolution simulation of an atomistic protein in MARTINI water

Julija Zavadlav et al.

JOURNAL OF CHEMICAL PHYSICS (2014)

Article Chemistry, Physical

Chemical potential of liquids and mixtures via adaptive resolution simulation

Animesh Agarwal et al.

JOURNAL OF CHEMICAL PHYSICS (2014)

Article Chemistry, Physical

Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations

Lin Shen et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

Article Chemistry, Physical

DNA Duplex Formation with a Coarse-Grained Model

Maciej Maciejczyk et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

Article Chemistry, Physical

A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment

Christopher Maffeo et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

Article Chemistry, Physical

Adaptive Resolution Simulation of MARTINI Solvents

Julija Zavadlav et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

Article Chemistry, Physical

Direct Mixing of Atomistic Solutes and Coarse-Grained Water

Mario Orsi et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

Article Chemistry, Physical

Molecular Dynamics Simulation of Aqueous Urea Solution: Is Urea a Structure Breaker?

Dibyendu Bandyopadhyay et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2014)

Review Chemistry, Multidisciplinary

The power of coarse graining in biomolecular simulations

Helgi I. Ingolfsson et al.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2014)

Article Computer Science, Interdisciplinary Applications

ESPResSo++: A modern multiscale simulation package for soft matter systems

Jonathan D. Halverson et al.

COMPUTER PHYSICS COMMUNICATIONS (2013)

Article Chemistry, Physical

A sequence-dependent rigid-base model of DNA

O. Gonzalez et al.

JOURNAL OF CHEMICAL PHYSICS (2013)

Article Chemistry, Physical

Perspective: Coarse-grained models for biomolecular systems

W. G. Noid

JOURNAL OF CHEMICAL PHYSICS (2013)

Article Chemistry, Physical

Coarse-Grained Simulations of RNA and DNA Duplexes

Tristan Cragnolini et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2013)

Article Chemistry, Physical

Water's Structure around Hydrophobic Solutes and the Iceberg Model

N. Galamba

JOURNAL OF PHYSICAL CHEMISTRY B (2013)

Article Physics, Multidisciplinary

Adaptive resolution simulation of salt solutions

Stas Bevc et al.

NEW JOURNAL OF PHYSICS (2013)

Article Physics, Multidisciplinary

Hamiltonian Adaptive Resolution Simulation for Molecular Liquids

Raffaello Potestio et al.

PHYSICAL REVIEW LETTERS (2013)

Article Physics, Multidisciplinary

Monte Carlo Adaptive Resolution Simulation of Multicomponent Molecular Liquids

Raffaello Potestio et al.

PHYSICAL REVIEW LETTERS (2013)

Review Chemistry, Physical

Coarse-grained molecular models of water: a review

Kevin R. Hadley et al.

MOLECULAR SIMULATION (2012)

Article Physics, Multidisciplinary

Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir

S. Fritsch et al.

PHYSICAL REVIEW LETTERS (2012)

Article Biophysics

Definition and testing of the GROMOS force-field versions 54A7 and 54B7

Nathan Schmid et al.

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (2011)

Article Chemistry, Physical

A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations

Sereina Riniker et al.

JOURNAL OF CHEMICAL PHYSICS (2011)

Article Chemistry, Physical

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

Thomas E. Ouldridge et al.

JOURNAL OF CHEMICAL PHYSICS (2011)

Article Physics, Mathematical

Statistical Physics Problems in Adaptive Resolution Computer Simulations of Complex Fluids

Matej Praprotnik et al.

JOURNAL OF STATISTICAL PHYSICS (2011)

Article Chemistry, Physical

A hybrid all-atom/coarse grain model for multiscale simulations of DNA

Matias Rodrigo Machado et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2011)

Article Chemistry, Physical

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites

Andrzej J. Rzepiela et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2011)

Article Chemistry, Physical

Communication: On the locality of Hydrogen bond networks at hydrophobic interfaces

Bradley P. Lambeth et al.

JOURNAL OF CHEMICAL PHYSICS (2010)

Article Chemistry, Physical

Coupling different levels of resolution in molecular simulations

Simon Poblete et al.

JOURNAL OF CHEMICAL PHYSICS (2010)

Article Chemistry, Physical

Another Coarse Grain Model for Aqueous Solvation: WAT FOUR?

Leonardo Darre et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)

Article Multidisciplinary Sciences

Chemically accurate coarse graining of double-stranded DNA

Alexey Savelyev et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Chemistry, Physical

Effects of bundling on the properties of the SPC water model

Marc Fuhrmans et al.

THEORETICAL CHEMISTRY ACCOUNTS (2010)

Article Biochemistry & Molecular Biology

3D-DART: a DNA structure modelling server

Marc van Dijk et al.

NUCLEIC ACIDS RESEARCH (2009)

Review Chemistry, Physical

Multiscale simulation of soft matter: From scale bridging to adaptive resolution

Matej Praprotnik et al.

ANNUAL REVIEW OF PHYSICAL CHEMISTRY (2008)

Article Chemistry, Physical

Coarse-grained molecular modeling of non-ionic surfactant self-assembly

Wataru Shinoda et al.

SOFT MATTER (2008)

Article Chemistry, Physical

The MARTINI force field: Coarse grained model for biomolecular simulations

Siewert J. Marrink et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2007)

Article Chemistry, Physical

Mixed atomistic and coarse-grained molecular dynamics: Simulation of a membrane-bound ion channel

Qiang Shi et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2006)

Article Chemistry, Physical

Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly

M Praprotnik et al.

JOURNAL OF CHEMICAL PHYSICS (2005)

Article Chemistry, Physical

Coarse grained model for semiquantitative lipid simulations

SJ Marrink et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2004)

Review Biochemistry & Molecular Biology

Molecular dynamics simulations of biomolecules

M Karplus et al.

NATURE STRUCTURAL BIOLOGY (2002)

Article Multidisciplinary Sciences

Relationship between structural order and the anomalies of liquid water

JR Errington et al.

NATURE (2001)