Related references
Note: Only part of the references are listed.A method to apply bond-angle constraints in molecular dynamics simulations
Maria Pechlaner et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2021)
Algorithms to apply dihedral-angle constraints in molecular or stochastic dynamics simulations
Maria Pechlaner et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
The Effect of Using a Twin-Range Cutoff Scheme for Nonbonded Interactions: Implications for Force-Field Parametrization?
Matthias Diem et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
The effect of different cutoff schemes in molecular simulations of proteins
Matthias Diem et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2020)
Polarization Effects in Simulations of Kaolinite-Water Interfaces
Edgar Galicia-Andres et al.
LANGMUIR (2019)
Influence of the Treatment of Nonbonded Interactions on the Thermodynamic and Transport Properties of Pure Liquids Calculated Using the 2016H66 Force Field
Yan M. H. Goncalves et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview
Sereina Riniker
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2018)
Anisotropic reaction field correction for long-range electrostatic interactions in molecular dynamics simulations
Dominik Sidler et al.
JOURNAL OF CHEMICAL PHYSICS (2018)
The Impact of Using Single Atomistic Long-Range Cutoff Schemes with the GROMOS 54A7 Force Field
Tomas F. D. Silva et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)
Validation of Molecular Simulation: An Overview of Issues
Wilfred F. van Gunsteren et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2018)
Real Cost of Speed: The Effect of a Time-Saving Multiple-Time-Stepping Algorithm on the Accuracy of Molecular Dynamics Simulations
Sabine Reisser et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)
Deriving Structural Information from Experimentally Measured Data on Biomolecules
Wilfred F. van Gunsteren et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2016)
A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set
Bruno A. C. Horta et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Picosecond to Millisecond Structural Dynamics in Human Ubiquitin
Kresten Lindorff-Larsen et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2016)
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop
Paul D. Adams et al.
STRUCTURE (2016)
On the use of a weak-coupling thermostat in replica-exchange molecular dynamics simulations
Zhixiong Lin et al.
JOURNAL OF CHEMICAL PHYSICS (2015)
Supra-Atomic Coarse-Grained GROMOS Force Field for Aliphatic Hydrocarbons in the Liquid Phase
Andreas P. Eichenberger et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Toward the correction of effective electrostatic forces in explicit-solvent molecular dynamics simulations: restraints on solvent-generated electrostatic potential and solvent polarization
Maria M. Reif et al.
THEORETICAL CHEMISTRY ACCOUNTS (2015)
Challenge of Representing Entropy at Different Levels of Resolution in Molecular Simulation
Wei Huang et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2015)
A Polarizable Empirical Force Field for Molecular Dynamics Simulation of Liquid Hydrocarbons
Oliwia M. Szklarczyk et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2014)
On the compatibility of polarisable and non-polarisable models for liquid water
Stephan Jan Bachmann et al.
MOLECULAR PHYSICS (2014)
The Seven Sins in Academic Behavior in the Natural Sciences
Wilfred F. van Gunsteren
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2013)
Multi-Resolution Simulation of Biomolecular Systems: A Review of Methodological Issues
Katharina Meier et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2013)
Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination
Alexander Wlodawer et al.
FEBS JOURNAL (2013)
Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects
Gabriel J. Rocklin et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
PDB_REDO: constructive validation, more than just looking for errors
Robbie P. Joosten et al.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2012)
Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation
Nathan Schmid et al.
COMPUTER PHYSICS COMMUNICATIONS (2012)
Validation of the GROMOS 54A7 Force Field Regarding Mixed α/β-Peptide Molecules
Dongqi Wang et al.
HELVETICA CHIMICA ACTA (2012)
On Hype, Malpractice, and Scientific Misconduct in Organic Synthesis
Rolf Carlson et al.
HELVETICA CHIMICA ACTA (2012)
Maintain rigid structures in Verlet based Cartesian molecular dynamics simulations
Peng Tao et al.
JOURNAL OF CHEMICAL PHYSICS (2012)
Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations
Jens Kleinjung et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field
Maria M. Reif et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
New functionalities in the GROMOS biomolecular simulation software
Anna-Pitschna E. Kunz et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2012)
Interfacing the GROMOS (bio)molecular simulation software to quantum-chemical program packages
Katharina Meier et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2012)
Thirty-five years of biomolecular simulation: development of methodology, force fields and software
Wilfred F. van Gunsteren et al.
MOLECULAR SIMULATION (2012)
On developing coarse-grained models for biomolecular simulation: a review
Sereina Riniker et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2012)
Definition and testing of the GROMOS force-field versions 54A7 and 54B7
Nathan Schmid et al.
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (2011)
Biomolecular structure refinement using the GROMOS simulation software
Nathan Schmid et al.
JOURNAL OF BIOMOLECULAR NMR (2011)
GROMOS plus plus Software for the Analysis of Biomolecular Simulation Trajectories
Andreas P. Eichenberger et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Validation of the GROMOS 54A7 Force Field with Respect to β-Peptide Folding
Wei Huang et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Molecular Dynamics with Multiple Time Scales: How to Avoid Pitfalls
Joseph A. Morrone et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
A New Force Field for Simulating Phosphatidylcholine Bilayers
David Poger et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2010)
Molecular Dynamics Simulations of a Reversibly Folding β-Heptapeptide in Methanol: Influence of the Treatment of Long-Range Electrostatic Interactions
Maria M. Reif et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
A Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics
David S. Cerutti et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)
Explicit-solvent molecular dynamics simulations of a DNA tetradecanucleotide duplex: lattice-sum versus reaction-field electrostatics
Vincent Kraeutler et al.
MOLECULAR SIMULATION (2008)
Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures
Alexander Wlodawer et al.
FEBS JOURNAL (2008)
On the calculation of velocity-dependent properties in molecular dynamics simulations using the leapfrog integration algorithm
Michel A. Cuendet et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
A multiple time step algorithm compatible with a large number of distance classes and an arbitrary distance dependence of the time step size for the fast evaluation of nonbonded interactions in molecular simulations
Vincent Kraeutler et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2006)
Computation of methodology-independent ionic solvation free energies from molecular simulations.: II.: The hydration free energy of the sodium cation
Mika A. Kastenholz et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Development of a lattice-sum method emulating nonperiodic boundary conditions for the treatment of electrostatic interactions in molecular simulations:: A continuum-electrostatics study
MA Kastenholz et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Biomolecular modeling: Goals, problems, perspectives
Wilfred F. van Gunsteren et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2006)
The GROMOS software for biomolecular simulation:: GROMOS05
M Christen et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
Combining the lattice-sum and reaction-field approaches for evaluating long-range electrostatic interactions in molecular simulations -: art. no. 034107
TN Heinz et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Validation of the 53A6 GROMOS force field
C Oostenbrink et al.
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (2005)
An approximate but fast method to impose flexible distance constraints in molecular dynamics simulations
M Christen et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Influence of artificial periodicity and ionic strength in molecular dynamics simulations of charged biomolecules employing lattice-sum methods
MA Kastenholz et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2004)
Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of hen egg lysozyme
TA Soares et al.
JOURNAL OF BIOMOLECULAR NMR (2004)
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
C Oostenbrink et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Increasing the time step and efficiency of molecular dynamics simulations: Optimal solutions for equilibrium simulations or structure refinement of large biomolecules
U Stocker et al.
MOLECULAR SIMULATION (2003)
Verlet-I/r-RESPA/Impulse is limited by nonlinear instabilities
Q Ma et al.
SIAM JOURNAL ON SCIENTIFIC COMPUTING (2003)
Derivation of an improved simple point charge model for liquid water:: SPC/A and SPC/L
A Glättli et al.
JOURNAL OF CHEMICAL PHYSICS (2002)
An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase
LD Schuler et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2001)
Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal
R Walser et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2001)
The GROMOS96 benchmarks for molecular simulation
AMJJ Bonvin et al.
COMPUTER PHYSICS COMMUNICATIONS (2000)
Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions:: Influence of artificial periodicity on peptide conformation
W Weber et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2000)
On the choice of dihedral angle potential energy functions for n-alkanes
LD Schuler et al.
MOLECULAR SIMULATION (2000)
Share Paper
