Cargando…

Coarse-grained and all-atom MD simulations with Gromacs based on CELLmicrocosmos 2.2 model membranes

Detalles Bibliográficos
Autores principales:	Sommer, B, Dingersen, T, Gamroth, C, Heissmann, AJ, Lukat, G, Rotzoll, R, Rubert, S, Schäfer, A, Krüger, J
Formato:	Texto
Lenguaje:	English
Publicado:	BioMed Central 2011
Materias:	Poster Presentation
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3083600/ http://dx.doi.org/10.1186/1758-2946-3-S1-P43

Ejemplares similares

The GMX-Plugin for the CELLmicrocosmos MembraneEditor
por: Rubert, Sebastian, et al.
Publicado: (2012)

CELLmicrocosmos 2.2: advancements and applications in modeling of three-dimensional PDB membranes
por: Sommer, Björn, et al.
Publicado: (2010)

Protocol for the development of coarse-grained structures for macromolecular simulation using GROMACS
por: Niranjan, Vidya, et al.
Publicado: (2023)

ForceGen: atomic covalent bond value derivation for Gromacs
por: Nash, Anthony, et al.
Publicado: (2017)

The CELLmicrocosmos Tools: A Small History of Java-Based Cell and Membrane Modelling Open Source Software Development
por: Sommer, Bjorn
Publicado: (2019)

Nanomechanics of β-rich proteins related to neuronal disorders studied by AFM, all-atom and coarse-grained MD methods
por: Mikulska, Karolina, et al.
Publicado: (2014)

Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models
por: Genheden, Samuel
Publicado: (2017)

Designing coarse grained-and atom based-potentials for protein-protein docking
por: Tobi, Dror
Publicado: (2010)

Structural Investigation of MscL Gating Using Experimental Data and Coarse Grained MD Simulations
por: Deplazes, Evelyne, et al.
Publicado: (2012)

Efficient Empirical Valence Bond Simulations with GROMACS
por: Oanca, Gabriel, et al.
Publicado: (2023)

All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5
por: Genheden, Samuel, et al.
Publicado: (2016)

NMR refinement and peptide folding using the GROMACS software
por: Sinelnikova, Anna, et al.
Publicado: (2021)

Scalable Constant pH Molecular Dynamics in GROMACS
por: Aho, Noora, et al.
Publicado: (2022)

Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
por: Wabik, Jacek, et al.
Publicado: (2013)

charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS
por: Wacha, András F., et al.
Publicado: (2023)

Polarizable Water Model for the Coarse-Grained MARTINI Force Field
por: Yesylevskyy, Semen O., et al.
Publicado: (2010)

SMOG@ctbp: simplified deployment of structure-based models in GROMACS
por: Noel, Jeffrey K., et al.
Publicado: (2010)

Solution structure of multi-domain protein ER-60 studied by aggregation-free SAXS and coarse-grained-MD simulation
por: Okuda, Aya, et al.
Publicado: (2021)

Coarse Grained Parallel Function Evaluation
por: Rulon, P, et al.
Publicado: (1992)

Chaos and coarse graining in statistical mechanics
por: Castiglione, Patrizia, et al.
Publicado: (2008)

The power of coarse graining in biomolecular simulations
por: Ingólfsson, Helgi I, et al.
Publicado: (2014)

Multiconfigurational Coarse-Grained Molecular Dynamics
por: Sharp, Morris E., et al.
Publicado: (2019)

Thermodynamics of the Coarse-Graining Master Equation
por: Schaller, Gernot, et al.
Publicado: (2020)

De Sitter stability and coarse graining
por: Markkanen, T.
Publicado: (2018)

Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems
por: Spijker, Peter, et al.
Publicado: (2010)

MkVsites: A tool for creating GROMACS virtual sites parameters to increase performance in all‐atom molecular dynamics simulations
por: Larsson, Per, et al.
Publicado: (2020)

Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS
por: Kutzner, Carsten, et al.
Publicado: (2011)

Gromita: A Fully Integrated Graphical User Interface to Gromacs 4
por: Sellis, Diamantis, et al.
Publicado: (2009)

Best bang for your buck: GPU nodes for GROMACS biomolecular simulations
por: Kutzner, Carsten, et al.
Publicado: (2015)

A GPU-Accelerated Fast Multipole Method for GROMACS: Performance and Accuracy
por: Kohnke, Bartosz, et al.
Publicado: (2020)

Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models
por: Jonikas, Magdalena A., et al.
Publicado: (2009)

A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation
por: Zheng, Wenjun, et al.
Publicado: (2015)

Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models
por: Na, Hyuntae, et al.
Publicado: (2015)

A New Mixed All-Atom/Coarse-Grained Model: Application to Melittin Aggregation in Aqueous Solution
por: Shelley, Mee Y., et al.
Publicado: (2017)

Asymmetric Periodic Boundary Conditions for All-Atom Molecular Dynamics and Coarse-Grained Simulations of Nucleic Acids
por: Erban, Radek, et al.
Publicado: (2023)

Coarse-Grained Modeling and Molecular Dynamics Simulations of Ca(2+)-Calmodulin
por: Nde, Jules, et al.
Publicado: (2021)

Ascertaining mesoscopic parameters for SARS-CoV-2 assembly from all atom and coarse-grained simulations of the associated membrane protein
por: McTiernan, Joseph, et al.
Publicado: (2023)

Coarse-Grained Simulation of Myosin-V Movement
por: Katsimitsoulia, Zoe, et al.
Publicado: (2012)

Multiscale Coarse-Graining of the Protein Energy Landscape
por: Hills, Ronald D., et al.
Publicado: (2010)

Coarse graining and first-order phase transitions
por: Berges, J., et al.
Publicado: (1996)

Cannot write session to /tmp/vufind_sessions/sess_5s2g692p85gm5119bvkfalcs32