PACKMOL: A package for building initial configurations for molecular dynamics simulations
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Summary
This work has developed a code able to pack millions of atoms, grouped in arbitrarily complex molecules, inside a variety of three‐dimensional regions, which can be intersections of spheres, ellipses, cylinders, planes, or boxes.
- Type
- article
- Published
- 2009-10-01
- Cited by
- 4,171
- References
- 36
- Access
- Open access
- OpenAlex
- https://openalex.org/W2003949305
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:264710429
Keywords
Molecular dynamics, Molecule, van der Waals force, Simple (philosophy), Type (biology)
References
- Numerical Simulation in Molecular Dynamics: Numerics, Algorithms, Parallelization, Applications
- Large-Scale Active-Set Box-Constrained Optimization Method with Spectral Projected Gradients
- Numerical methods for unconstrained optimization and nonlinear equations
- Comparison of Cyclodextrin‐Dipeptide Inclusion Complexes in the Absence and Presence of Urea by Means of Capillary Electrophoresis, Nuclear Magnetic Resonance and Molecular Modeling
- An evaluation of non-periodic boundary condition models in molecular dynamics simulations using prion octapeptides as probes
- Molecular dynamics simulations of angiotensin II in aqueous and dimethyl sulfoxide environments.
- Computational study on the properties and structure of methyl lactate.
- Computational study of the binding affinity and selectivity of the bacterial ammonium transporter AmtB.
- Ligand binding to the voltage-gated Kv1.5 potassium channel in the open state--docking and computer simulations of a homology model.
- A new trust region algorithm for bound constrained minimization
- Effect of ionic solutes on the hydrogen bond network dynamics of water: power spectral analysis of aqueous NaCl solutions.
- Molecular dynamics simulations of Cu(II) and the PHGGGWGQ octapeptide.
- Solvation Dynamics at the Water/Zirconia Interface: Molecular Dynamics Simulations†
- Molecular dynamics simulations of ligand dissociation from thyroid hormone receptors: evidence of the likeliest escape pathway and its implications for the design of novel ligands.
- On the properties of 1-butyl-3-methylimidazolium octylsulfate ionic liquid
- Properties and structure of aromatic ester solvents.
- Molecular dynamics simulation of the ionic liquid N-ethyl-N,N-dimethyl-N-(2-methoxyethyl)ammonium bis(trifluoromethanesulfonyl)imide.
- Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking
- Molecular dynamics analysis of the AOT/water/isooctane system: Effect of simulation time, initial configuration, and model salts
- A fast algorithm for particle simulations
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- Best Practices for Foundations in Molecular Simulations [Article v1.0]
- How atomic level interactions drive membrane fusion: Insights from molecular dynamics simulations
- Solvent effects and driving forces in pillararene inclusion complexes.
- Modeling the self-assembly of ordered nanoporous materials
- Multiscale simulations of protein dynamics
- Membrane interaction of the factor VIIIa discoidin domains in atomistic detail
- Dry-Surface Simulation Method for the Determination of the Work of Adhesion of Solid-Liquid Interfaces.
- Helix 12 dynamics and thyroid hormone receptor activity: experimental and molecular dynamics studies of Ile280 mutants.
- The pattern of xylan acetylation suggests xylan may interact with cellulose microfibrils as a twofold helical screw in the secondary plant cell wall of Arabidopsis thaliana
- Multiscale molecular dynamics simulations of sodium dodecyl sulfate micelles: from coarse-grained to all-atom resolution
- Membrane permeation induced by aggregates of human islet amyloid polypeptides.
- Separable cubic modeling and a trust-region strategy for unconstrained minimization with impact in global optimization
- Avogadro: an advanced semantic chemical editor, visualization, and analysis platform
- Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools
- Mass spectrometry - From peripheral proteins to membrane motors
- Characterizing the Membrane-Bound State of Cytochrome P450 3A4: Structure, Depth of Insertion, and Orientation
- Sparse Projected-Gradient Method As a Linear-Scaling Low-Memory Alternative to Diagonalization in Self-Consistent Field Electronic Structure Calculations.
- Mesoscale phenomena in ternary solutions of tertiary butyl alcohol, water, and propylene oxide.
- Packing circles within ellipses
- Formation of Raft-Like Assemblies within Clusters of Influenza Hemagglutinin Observed by MD Simulations
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