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conjugate-gradient energy minimization  (Molecular Dynamics Inc)

 
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    Molecular Dynamics Inc conjugate-gradient energy minimization
    Conjugate Gradient Energy Minimization, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/conjugate+gradient+minimization/conjugate+gradient+algorithm/pmc06333101-441-6-10
    Average 90 stars, based on 1 article reviews
    conjugate-gradient energy minimization - by Bioz Stars, 2026-11
    90/100 stars

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    Article Title: Viscoelastic Response in Hydrous Polymers: The Role of Hydrogen Bonds and Microstructure
    Article Snippet: Prior to Molecular Dynamics (MD) simulation, these initial configurations were quasi- statically relaxed to a local minimum-energy configuration through conjugate gradient method, in which the energy and force tolerances were set to be 1.0 × 10-4 Kcal/mol and 1.0 × 10-4 Kcal/(mol·Å), respectively.

    Article Title: A dual histone code specifies the binding of heterochromatin protein Rhino to a subset of piRNA source loci
    Article Snippet: MD simulations were performed according to the following steps: (1) Minimization was performed with a maximum cycle of 5000 and with the steepest descent algorithm for the first 2500 cycles, with a periodic boundary for constant volume (canonical ensemble, NVT) and without the SHAKE (an algorithm for constrained molecular dynamics) algorithm activated.

    Article Title: Distinct conformations of the HIV-1 V3 loop crown are targetable for broad neutralization
    Article Snippet: The systems were first minimized by 2000 conjugate gradient steps, followed by a free molecular dynamics simulation with a hydrogen mass repartitioning scheme to achieve a timestep of 4 fs.

    Article Title: A computational algorithm to assess the physiochemical determinants of T cell receptor dissociation kinetics
    Article Snippet: Generating equilibrated starting structures for the Steered Molecular Dynamics simulations required four steps: Steepest descent energy minimization to ensure correct geometry and the absence of steric clashes; 100 ps simulation in the constant volume (NVT) ensemble to bring atoms to correct kinetic energies, while maintaining temperature at 310 K by coupling all protein and non-protein atoms to separate baths using the velocity rescale thermostat with a 0.1 ps time constant , 100 ps simulation in the constant pressure (NPT) ensemble using Berendsen pressure coupling and a 2.0 ps time constant to maintain isotropic pressure at 1.0 bar; and Production MD simulations conducted for 50–150 ns with no restraints.

    Article Title: Self-Adhesive and Conductive Dual-Network Polyacrylamide Hydrogels Reinforced by Aminated Lignin, Dopamine, and Biomass Carbon Aerogel for Ultrasensitive Pressure Sensor.
    Article Snippet: Molecular dynamics simulation and calculation Before calculation, the energy minimization processing was performed using the steepest descent algorithm and the conjugate gradient algorithm.

    Article Title: DNA facilitates heterodimerization between human transcription factors FoxP1 and FoxP2 by increasing their conformational flexibility
    Article Snippet: These structures were initially energy minimized using a gradient descent algorithm from the molecular dynamics suite Amber20, and subsequently, energy minimized using the Newton-Raphson algorithm through the NAB module of Amber until reaching a Δrms of 10 −12 .

    Software:

    Article Title: Combined Experimental and Computational Study of Polycyclic Aromatic Compound Aggregation: The Impact of Solvent Composition
    Article Snippet: .. Molecular dynamics (MD) simulations were carried out using the GROMACS 4.6.5 software package.5,42,57,58 Starting from an initial energy minimization procedure using the steepest descent algorithm (104 iterations, convergence criterion of 25 kJ/mol/nm and initial step size of 0.01 nm),59 short sequential simulations (0.1 and 3.0 ns, respectively) in the NVT and NPT ensembles were used to relax the systems. ..



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