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namd software (Molecular Dynamics Inc)

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Molecular Dynamics Inc namd software
Namd Software, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/dynamics+simulation+namd+software/namd+software/pmc12837360-142-17-0
Average 86 stars, based on 1 article reviews

namd software - by Bioz Stars, 2026-11

86/100 stars

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Article Title: Mechanical response of the Reca nucleoprotein filament to increasing D-loop length
Article Snippet: .. Molecular dynamics (MD) simulations were performed on all systems using the NAMD software[ ], versions 2.12 and 2.13, and the CHARMM36m force field including the CMAP correction [ ] under periodic boundary conditions with the Particle Mesh Ewald (PME) method [ ]. ..

Article Title: Collective interactions along recombinase-bound D-loops could speed repair of double-strand breaks by destabilizing flanking homoduplex tails.
Article Snippet: .. Molecular dynamics (MD) simulations were performed on all systems using the NAMD software [ 44 ] versions 2.12 and 2.13, and the CHARMM36m force field including the CMAP correction [ 46 ] and using the Particle Mesh Ewald (PME) method to account for long-range electrostatic interactions [ 47 ]. ..

Article Title: Neuroprotective Effect of D-Pinitol Against MPTP-Induced Parkinsonism in C57BL/6J Mice
Article Snippet: .. Molecular dynamics simulations evaluated the evolution and stability of the optimal molecular docking positions by using the NAMD software (version 3.0.1) [ ]. .. The CHARMM-GUI [ ] and Solution Builder [ ] modules, employing the CHARMM36 force field, performed the complex parameterization [ ].

Article Title: Development and Immunogenicity Assessment of a Multi-Epitope Antigen Against Zika Virus: An In Silico and In Vivo Approach
Article Snippet: Docking simulations were visualized and analyzed using Biovia Discovery Studio [ ]. .. To evaluate the temporal stability of the epitope–HLA complexes predicted by docking, Molecular Dynamics (MD) simulations were performed using the NAMD 3.0 software [ ], utilizing the computational resources provided by the “National Center for High Performance Processing in São Paulo (CENAPAD-SP). .. The complexes were parameterized using the CHARMM-GUI server [ ].

Article Title: High throughput stochastic bio-molecular sensor
Article Snippet: .. Molecular dynamics (MD) simulations were performed with NAMD software using periodic boundary conditions. ..

Article Title: Neuroprotective Effect of D-Pinitol Against MPTP-Induced Parkinsonism in C57BL/6J Mice.
Article Snippet: .. Molecular dynamics simulations evaluated the evolution and stability of the optimal molecular docking positions by using the NAMD software (version 3.0.1) [32]. .. The CHARMM-GUI [33] and Solution Builder [34] modules, employing the CHARMM36 force field, performed the complex parameterization [35].

Article Title: pH-induced changes in hydrophobicity and key amino acid exposure regulate myoglobin digestibility
Article Snippet: The original structure was visualized and optimized using the Visual Molecular Dynamics (VMD) software. .. Molecular dynamics (MD) simulations were performed using the NAMD 2.14 software with the CHARMM27 force field , and simulations were carried out under different pH conditions. ..

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namd software (Molecular Dynamics Inc)

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