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Molecular Dynamics Inc amber program package
Amber Program Package, 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/amber+program+package/package+program/pmc13009001-49-27-3
Average 86 stars, based on 1 article reviews
amber program package - by Bioz Stars, 2026-09
86/100 stars

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Article Title: [2602.04606] Structures of iron and cobalt bimetallic clusters for optimized chemical vapor deposition growth of single-walled carbon nanotubes
Article Snippet: Molecular dynamics (MD) simulations were carried out using the Graphics Processing Units Molecular Dynamics (GPUMD) software46 version 4.2.

Article Title: Supporting Information Conformational Properties of Equilenin-DNA Adducts: Stereoisomer and Base Effects
Article Snippet: Supporting Information Conformational Properties of Equilenin-DNA Adducts: Stereoisomer and Base Effects Shuang Ding†, Robert Shapiro‡, Nicholas E. Geacintov‡, and Suse Broyde†,* † Department of Biology and ‡Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA E-mail: broyde@nyu.edu Running Title: Equilenin DNA Adducts: Stereoisomer and Base Effects *Corresponding author: Suse Broyde, tel. (212)998-8231, fax (212)995-4015, email broyde@nyu.edu Molecular Dynamics Protocol The AMBER 7 program package (35) the Cornell et al. force field (36) and the parm99.dat parameter set (37) were employed to perform MD simulations of the 4- OHEN-G adducts.

Article Title: STable AutoCorrelation Integral Estimator: Robust and Accurate Transport Properties from Molecular Dynamics Simulations.
Article Snippet: STACIE (STable AutoCorrelation Integral Estimator) is a novel algorithm and Python package that delivers robust, uncertainty-aware estimates of autocorrelation integrals from timecorrelated data.. While its primary application is deriving transport properties from equilibrium molecular dynamics simulations, STACIE is equally applicable to time-correlated data in other scientific fields.. A key feature of STACIE is its ability to provide robust and accurate estimates without requiring manual adjustment of hyperparameters.

Article Title: STable AutoCorrelation Integral Estimator: Robust and Accurate Transport Properties from Molecular Dynamics Simulations
Article Snippet: [10] G. R. Kneller, V. Keiner, M. Kneller, and M. Schiller, “nMOLDYN: A program package for a neutron scattering oriented analysis of Molecular Dynamics simulations,” Comput.

Software:

Article Title: Computational modeling of PROTAC ternary complexes as ensembles using SILCS-xTAC
Article Snippet: .. Molecular dynamics simulations were performed with Gromacs version 2023 59 , 60 and SILCS software version 2024 (SilcsBio LLC). ..

Article Title: Virtual screening of compounds for the development of thyroid hormone analogues for potential application in cardiac regeneration
Article Snippet: .. Continuing the screening, Molecular Dynamics simulations were performed with NAMD program ( ) and Free Energy of Binding by Molecular Mechanics/Poisson–Boltzmann Surface Area (MM/PBSA) were calculated with AMBER program package ( ) (details in Sect. and ), semiempirical Quantum Mechanics, PM7 , and hybrid Quantum Mechanics Molecular Mechanics (QMMM) (B3LYP 6-31G*/CHARMM36) were calculated with Orca 5 software ( ) (details in 2.9 Quantum Mechanics Molecular Mechanics Hybrid Calculation). ..

Binding Assay:

Article Title: Virtual screening of compounds for the development of thyroid hormone analogues for potential application in cardiac regeneration
Article Snippet: .. Continuing the screening, Molecular Dynamics simulations were performed with NAMD program ( ) and Free Energy of Binding by Molecular Mechanics/Poisson–Boltzmann Surface Area (MM/PBSA) were calculated with AMBER program package ( ) (details in Sect. and ), semiempirical Quantum Mechanics, PM7 , and hybrid Quantum Mechanics Molecular Mechanics (QMMM) (B3LYP 6-31G*/CHARMM36) were calculated with Orca 5 software ( ) (details in 2.9 Quantum Mechanics Molecular Mechanics Hybrid Calculation). ..



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