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PACKMOL: A package for building initial configurations for molecular dynamics simulations

L. Martínez, R. Andrade, E. G. Birgin, J. M. Martínez
2009 Journal of Computational Chemistry  
Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure.  ...  The packing time for state-of-the-art molecular dynamics systems varies from a few seconds to a few minutes in a personal computer.  ...  Acknowledgements The authors thank the Brazilian national funding agencies CAPES and CNPq and the state of São Paulo agency FAPESP for financial support.  ... 
doi:10.1002/jcc.21224 pmid:19229944 fatcat:wqukrytub5hcpbgov7gfkckeuq

Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking

José Mario Martínez, Leandro Martínez
2003 Journal of Computational Chemistry  
Molecular Dynamics is a powerful methodology for the comprehension at molecular level of many chemical and biochemical systems.  ...  The initial configuration is chosen in such a way that the minimum distance between atoms of different molecules is greater than a fixed tolerance.  ...  Acknowledgments We are indebted to two anonymous referees for useful comments that helped us to improve this article.  ... 
doi:10.1002/jcc.10216 pmid:12692791 fatcat:ghoruuxahng3rkq7wosxg4xxde

Micelle Maker: An Online Tool for Generating Equilibrated Micelles as Direct Input for Molecular Dynamics Simulations

Dennis M. Krüger, Shina C. L. Kamerlin
2017 ACS Omega  
Here, we present a new Web server, Micelle Maker, which can provide equilibrated micelle models as a direct input for subsequent molecular dynamics simulations from a broad range of lipids (currently 25  ...  The spherical geometry and the dynamical behavior of micelles makes generating micelle structures for use in molecular simulations challenging.  ...  Another valuable tool is Packmol, 8 which is a command line tool to generate initial configurations for MD simulations using a packing optimization algorithm. 9 Packmol Table 1 .  ... 
doi:10.1021/acsomega.7b00820 pmid:28884160 pmcid:PMC5579539 fatcat:rlrsleefj5dhvipuigeqhscjky

DLPGEN: The Route to Prepare Molecular Dynamics Simulations [article]

Carlos Eduardo Sabino Bernardes
2022 Zenodo  
As an alternative to these options, PACKMOL can also be automatically called from DLPGEN to create simulation boxes for liquids. The program can handle force fields like OPLS, CHARMM, and AMBER.  ...  DLPGEN is a Fortran program that produces input files for DL_POLY, GROMACS, LAMMPS, and CHARMM.  ...  PACKMOL n entry Set constraints for a given molecular type while using Packmol. n position of the molecular type to which constraints will be used. entry constraint defined as in the Packmol manual (https  ... 
doi:10.5281/zenodo.6369274 fatcat:7ue3vokwc5d7tgjyzpuu4ayghq

Atomistic simulation studies of the α/β-glucoside and galactoside in anhydrous bilayers: effect of the anomeric and epimeric configurations

Sara Ahmadi, Vijayan Manickam Achari, HockSeng Nguan, Rauzah Hashim
2014 Journal of Molecular Modeling  
6/22/2014 Atomistic simulation studies of the α/β-glucoside and galactoside in anhydrous bilayers: effect of the anomeric and epimeric configurations -Springer Abstract Fully atomistic molecular dynamics  ...  and galactoside in anhydrous bilayers: effect of the anomeric and epimeric configurations Journal Journal of Molecular Modeling  ...  Martínez L, Andrade R, Birgin EG, Martínez JM (2009) Packmol: A package for building initial configurations for molecular dynamics simulations. J Comput Chem 30(13):2157-2164 CrossRef 31.  ... 
doi:10.1007/s00894-014-2165-0 pmid:24623320 fatcat:tsm3qa236nhs7br2mxezpzq5sq

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek, Geoffrey R Hutchison
2012 Journal of Cheminformatics  
dynamics simulations.  ...  Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages.  ...  We thank SourceForge for providing resources for issue tracking and managing releases, Launchpad for hosting language translations, and Kitware for additional dashboard resources.  ... 
doi:10.1186/1758-2946-4-17 pmid:22889332 pmcid:PMC3542060 fatcat:e2mdy6dfjfai5gcnexaaiyvjg4

Application of Molecular Dynamics Simulation to Small Systems [chapter]

Vctor M., Isabel Senz-Taver
2012 Molecular Dynamics - Theoretical Developments and Applications in Nanotechnology and Energy  
Most MD packages, such as GROMACS or AMBER, provide their own utilities for building starting configurations.  ...  Software that implements molecular dynamics simulation AMBER (Case, 2005; 2010; Pearlman, 1995) designates two different things: a force-field and a package for MD simulation.  ... 
doi:10.5772/35741 fatcat:rwx37rhiyvdbdjc65dwq2bjvxu

An Interactive Polymer Building Toolkit for Molecular Dynamics Simulations: PolyMAPS [article]

Xiaoli Yan, Santanu Chaudhuri
2022 arXiv   pre-print
PolyMAPS is an open-source library that helps researchers to initialize LAMMPS molecular dynamics simulations.  ...  PolyMAPS enables users to build small or polymeric molecules in a user-friendly interactive 3D plotting system that supports reading and writing systems in LAMMPS data file format.  ...  Introduction Many open-source preprocessing tools are developed for molecular dynamics (MD) simulations for simulation software such as LAMMPS, GROMACS [3] , CP2K [4] , etc.  ... 
arXiv:2204.14218v1 fatcat:iubd7evxxfflddmucjsdam4buy

CeMEAI: The Brazilian Center and Its Mathematics Research for Industry

E. G. Birgin, J. A. Cuminato, J. M. Martínez, T. Pereira
2017 Notices of the American Mathematical Society  
Industrial Applications Building Initial Configurations for Molecular Dynamics Simulations-Packmol Molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way  ...  Figure 1 . 1 Molecular systems built with Packmol for molecular dynamics simulations: Left: a protein solvated with a mixture of water (red) and glucose (green); Center: a spherical lipid vesicle with  ... 
doi:10.1090/noti1513 fatcat:r3qlq7zenjbnth26ykwer5y3ju

Roadmap for Computer-Aided Modeling of Theranostics and Related Nanosystems

Jozef Ulicny, Tibor Kozar, Gh. Adam, J. Buša, M. Hnatič, D. Podgainy
2018 EPJ Web of Conferences  
Detailed understanding of the interactions of novel metal-containing nanoparticles with biological membranes, macromolecules and other molecular targets of the living cell is crucial for the elucidation  ...  We present here the construction and modeling of thiolate-protected gold clusters and the prediction of their static and dynamic properties.  ...  Marian Antalik (IEP SAS) for experimental support and discussions on the functionalized NPs.  ... 
doi:10.1051/epjconf/201817305017 fatcat:72posd2k6vhbfcxii4jw6bvyqa

MEMBRANE PACKING PROBLEMS: A SHORT REVIEW ON COMPUTATIONAL MEMBRANE MODELING METHODS AND TOOLS

Björn Sommer
2013 Computational and Structural Biotechnology Journal  
I personally would like to thank the referees who helped me to improve the quality of this publication and Anette Hall, University of Eastern Finland, who provided me with a very nice Packmol example script  ...  Acknowledgements This work was supported in part by: The Graduate College for Bioinformatics (GK635, which is sponsored by the Deutsche Forschungsgemeinschaft, DFG).  ...  Then, a grid-based implicit force field is used during a subsequent Molecular Dynamics simulation.  ... 
doi:10.5936/csbj.201302014 pmid:24688707 pmcid:PMC3962210 fatcat:hr4lrwozifdkdb73sazlae3gtu

NaRIBaS—A Scripting Framework for Computational Modeling of Nanomaterials and Room Temperature Ionic Liquids in Bulk and Slab

Eva Roos Nerut, Karl Karu, Iuliia Voroshylova, Kathleen Kirchner, Tom Kirchner, Maxim Fedorov, Vladislav Ivaništšev
2018 Computation  
Three examples are given to illustrate the NaRIBaS workflows for density functional theory (DFT) calculations of ionic pairs, molecular dynamics (MD) simulations of bulk ionic liquids (ILs), and MD simulations  ...  This article introduces NaRIBaS (Nanomaterials and Room Temperature Ionic Liquids in Bulk and Slab)—a scripting framework that combines bash scripts with computational codes to ease modeling of nanomaterials  ...  Acknowledgments: We thank Isabel Lage-Estebanez for preparing the force fields files used in this work. We thank Samuel W. Coles and Borja Docampo-Álvarez for validation of NaRIBaS scripts.  ... 
doi:10.3390/computation6040057 fatcat:wfc63vrjpbd6ne3zvu6w52ivtu

Matriarch: A Python Library for Materials Architecture

Tristan Giesa, Ravi Jagadeesan, David I. Spivak, Markus J. Buehler
2015 ACS Biomaterials Science & Engineering  
Current software for materials engineering allows the user to specify polypeptide chains and simple secondary structures prior to molecular dynamics simulation, but is not flexible in terms of the geometric  ...  Matriarch can be used in tandem with molecular dynamics simulations and helps engineers design and modify biologically inspired materials based on their desired functionality.  ...  Matriarch returns PDB files that can be used as a starting point for molecular dynamics simulations.  ... 
doi:10.1021/acsbiomaterials.5b00251 pmid:27570830 pmcid:PMC4996638 fatcat:dqm47rnqxff3pktb24njs4ecsq

Atomistic simulations of amorphous polymers in the cloud with PolymerModeler [article]

Benjamin P. Haley, Chunyu Li, Nathaniel Wilson, Eugenio Jaramillo, Alejandro Strachan
2015 arXiv   pre-print
We introduce Poly- merModeler, a general-purpose, online simulation tool to build atomistic structures of amorphous polymers and perform MD simulations on the re- sulting configurations to predict their  ...  Molecular dynamics (MD) simulations enable the description of ma- terial properties and processes with atomistic detail by numerically solv- ing the time evolution of every atom in the system.  ...  The authors also thank David Lowing for testing the glass transition calculations.  ... 
arXiv:1503.03894v1 fatcat:tgpcqmgetbgajna2xxucvzemum

The Molecular Simulation Design Framework (MoSDeF): Capabilities and Applications [article]

Peter Cummings
2020 figshare.com  
Presentation given at 2019 International Workshop on Molecular Simulation, Hangzhou, China, October 12-13, 2019  ...  Forcefield Atom-Typing for Molecular Simulation o NSF CSSI OAC 1835874: Collaborative Research: NSCI Framework: Software for Building a Community-Based Molecular Modeling Capability Around the Molecular  ...  K. et al. (2013) Nuzzo et al., JACS, 1983, 105 q In molecular dynamics simulation, we save numerically some variant of Newton's equations q Potential energy is described by a force field with as many  ... 
doi:10.6084/m9.figshare.13024619.v1 fatcat:teq3wg6bojbvrlao5iv5q6jfwe
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