'Tinker-OpenMM : Absolute and Relative Alchemical Free Energies using AMOEBA on GPUs'.
'Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields'. Harger, Matthew Torabifard, Hedieh Cisneros, Andrés Schnieders, Michael Gresh, Nohad Maday, Yvon Ren, Pengyu Ponder, Jay Piquemal, Jean-Philip (2018). Lagardère, Louis Jolly, Luc-Henri Lipparini, Filippo Aviat, Félix Stamm, Benjamin Jing, Zhifeng F.global optimizing via energy surface smoothing, including a Potential Smoothing and Search (PSS) method.fitting of intermolecular potential parameters to structural and thermodynamic data.free energy calculations via free energy perturbation or weighted histogram analysis.
Tinkertool system 2 serial full#
full energy surface search via a Conformation Scanning method.location of a transition state between two minima.verification of analytical derivatives of standard and user defined potentials.analysis and breakdown of single point potential energies.simulated annealing with various cooling protocols.building protein and nucleic acid structures from sequence.distance geometry including an efficient random pairwise metrization.molecular, stochastic, and rigid body dynamics with periodic boundaries and control of temperature and pressure.energy minimizing over Cartesian coordinates, torsional angles, or rigid bodies via conjugate gradient, variable metric or a truncated Newton method.Programs are provided to perform many functions including:
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