New functionalities in the GROMOS biomolecular simulation software (Q57235426)

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16 January 2020

title

New functionalities in the GROMOS biomolecular simulation software (English)

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16 January 2020

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16 January 2020

Daan P Geerke

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16 January 2020

Bruno A C Horta

4

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16 January 2020

Philippe H Hünenberger

5

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16 January 2020

Sereina Riniker

6

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16 January 2020

Wilfred F van Gunsteren

8

object named as

Wilfred F van Gunsteren

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16 January 2020

author name string

Nathan Schmid

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16 January 2020

Anna-Pitschna E Kunz

1

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16 January 2020

publication date

11 November 2011

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Journal of Computational Chemistry

16 January 2020

published in

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volume

33

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issue

3

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page(s)

340-353

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The GROMOS software for biomolecular simulation: GROMOS05.

16 January 2020

cites work

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Accounting for polarization in molecular simulation

21 January 2018

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A refined, efficient mean solvation force model that includes the interior volume contribution

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

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On the Calculation of the Dielectric Permittivity and Relaxation of Molecular Models in the Liquid Phase

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Charge-on-spring polarizable water models revisited: From water clusters to liquid water to ice

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Development of a nonlinear classical polarization model for liquid water and aqueous solutions: COS/D.

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Molecular mechanics in biology: from structure to function, taking account of solvation

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21 January 2018

Implicit solvent models

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Recent advances in the development and application of implicit solvent models in biomolecule simulations

21 January 2018

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Recent advances in implicit solvent-based methods for biomolecular simulations

21 January 2018

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Hydrophobic bonding and accessible surface area in proteins

21 January 2018

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Solvation energy in protein folding and binding

21 January 2018

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Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides

21 January 2018

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Semianalytical treatment of solvation for molecular mechanics and dynamics

21 January 2018

1 reference

Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects

21 January 2018

1 reference

Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor

21 January 2018

1 reference

Inclusion of solvation free energy with molecular mechanics energy: Alanyl dipeptide as a test case

21 January 2018

1 reference

Atomic solvation parameters applied to molecular dynamics of proteins in solution

21 January 2018

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Effective energy function for proteins in solution

21 January 2018

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Evaluation of a fast implicit solvent model for molecular dynamics simulations

21 January 2018

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Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome

21 January 2018

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Rapid Estimation of Solvation Energy for Simulations of Protein-Protein Association

21 January 2018

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The importance of solute-solvent van der Waals interactions with interior atoms of biopolymers.

21 January 2018

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AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

21 January 2018

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Strong solute-solute dispersive interactions in a protein-ligand complex

21 January 2018

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Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms

21 January 2018

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Analytical approximation to the accessible surface area of proteins.

21 January 2018

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Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

The GROMOS Biomolecular Simulation Program Package

21 January 2018

1 reference

Lennard-Jones Viscosities in Wide Ranges of Temperature and Density: Fast Calculations Using a Steady–State Periodic Perturbation Method

21 January 2018

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Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

An Efficient Mean Solvation Force Model for Use in Molecular Dynamics Simulations of Proteins in Aqueous Solution

21 January 2018

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Peptide folding simulations: no solvent required?

21 January 2018

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21 January 2018

Identifiers

DOI

10.1002/JCC.21954

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journals/jcc/KunzAGHHRSG12

16 January 2020

DBLP publication ID

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DBLP Dataset 2021-01-02

28 January 2021

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