Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
1992/10/01 by Shuichi Miyamoto, Peter A. Kollman · 45 citations
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Protein Structure and Dynamics #Scientific Research and Discoveries #Spectroscopy and Quantum Chemical Studies
paper · doi:10.1002/jcc.540130805
Abstract
Abstract An analytical algorithm, called SETTLE, for resetting the positions and velocities to satisfy the holonomic constraints on the rigid water model is presented. This method is still based on the Cartesian coordinate system and can be used in place of SHAKE and RATTLE. We implemented this algorithm in the SPASMS package of molecular mechanics and dynamics. Several series of molecular dynamics simulations were carried out to examine the performance of the new algorithm in comparison with the original RATTLE method. It was found that SETTLE is of higher accuracy and is faster than RATTLE with reasonable tolerances by three to nine times on a scalar machine. Furthermore, the performance improvement ranged from factors of 26 to 98 on a vector machine since the method presented is not iterative. © 1992 by John Wiley & Sons, Inc.
Citations
Cited by
- Enhanced sampling and cryo-EM data resolve magnesium binding to RNA
- Conformational Profile of Galactose‐α‐1,3‐Galactose (α‐Gal) and Structural Basis of Its Immunological Response
- A nanopore-gated sub-attoliter silicon nanocavity for single-molecule trapping and analysis
- Characteristics of mono-, di-, and trivalent cations in electric double layers: a molecular dynamic investigation
- Large-Scale Molecular Dynamics Simulations for Highly Parallel Infrastructures
- Conformational preorganization of neighbouring groups modulates and expedites polymer self-deconstruction
- LINCS: A linear constraint solver for molecular simulations
- Long-range dispersion effects on the water/vapor interface simulated using the most common models
- Translocation of linearized full-length proteins through an engineered nanopore under opposing electrophoretic force
- Optimization of parameters for molecular dynamics simulation using smooth particle‐mesh Ewald in GROMACS 4.5
- The Effect of Microwaves on Protein Structure: Molecular Dynamics Approach
- The mycotoxin Beauvericin is an uncompetitive inhibitor of Cathepsin B
- The Kink-Turn Motif: A Powerful Test for Revealing Weaknesses in RNA Force Fields
- BindFlow: A Free, User-Friendly Pipeline for Absolute Binding Free Energy Calculations Using Free Energy Perturbation or MM(PB/GB)SA
- Biomolecular Modeling: Goals, Problems, Perspectives
- Ligand‐driven modulation of chaperone–cochaperone networks shapes proteostasis outcomes
- Large-scale energy decomposition for the analysis of protein stability
- Extensive structural change of the envelope protein of dengue virus induced by a tuned ionic strength: conformational and energetic analyses
- GROMACS: Fast, flexible, and free
- AlphaFold3 prediction of protein-protein complex: Is it ready for thermodynamic analysis?
- Structural basis of broad protection against influenza virus by human antibodies targeting the neuraminidase active site via a recurring motif in CDR H3
- Adsorption kinetic of myoglobin on mica and silica – Role of electrostatic interactions
- Formation of Sodium Chloride on the Surface of Sulfate-Rich Gobi Desert Salt in Response to Water Adsorption
- Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes
- When does molecular dynamics improve RNA models? Insights from CASP15 and practical guidelines
- Molecular dynamics simulations unveil the aggregation patterns and salting out of polyarginines at zwitterionic POPC bilayers in solutions of various ionic strengths
- Unraveling the effect of water and ethanol on ibuprofen nanoparticles formation
- Rational Design Principles for <i>De Novo</i> α-Helical Peptide Barrels with Dynamic Conductive Channels
- Contextualising the developability risk of antibodies with lambda light chains using enhanced therapeutic antibody profiling
- Guanidinium Like‐Charge Ion Pairing and Oligoarginine Aggregation in Water by Nuclear Magnetic Resonance, Cryo‐Electron Microscopy, and Molecular Dynamics
- Characterizing the Diversity of the CDR-H3 Loop Conformational Ensembles in Relationship to Antibody Binding Properties
- Structure-based identification of potent VEGFR-2 inhibitors from in vivo metabolites of a herbal ingredient
- Ion-Mediated Adsorption of Amyloid-β Peptides at the Liquid/Liquid Interface: Insights from Electrochemistry and Molecular Dynamics Simulations
- Replacement of a single residue in an antibody abolishes cognate antigen binding, as predicted by theoretical methods
- Effects of Conformational Sampling on Computing Redox Properties Using Linear Response Approach
- Medienpolitik: Gepflegtes Desinteresse
- Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficient
- Flexibility in PAM recognition expands DNA targeting in xCas9
- A unified framework for data-driven construction of stochastic reduced models with state-dependent memory
- A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations
- Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models
- Enhanced premelting at the ice-rubber interface using all-atom molecular dynamics simulation
- Copper, BDNF and Its N‐terminal Domain: Inorganic Features and Biological Perspectives
- The role of ATP in solubilizing RNA-binding protein fused in sarcoma.
- The jojoba lipid droplet protein LDAP1 facilitates the packaging of wax esters into lipid dropletsy
Related