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  • GaMD | Miao Lab - UNC School of Medicine
    Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for simultaneous unconstrained enhanced sampling and free energy calculations of biomolecules It works by adding a harmonic boost potential to smooth biomolecular potential energy surface and reduce energy barriers
  • Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced . . .
    Here, a Gaussian accelerated molecular dynamics (GaMD) approach is presented to reduce the energetic noise for simultaneous unstrained enhanced sampling and free energy calculation of biomolecules, even for large proteins
  • Gaussian accelerated molecular dynamics (GaMD): principles and . . .
    Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for simultaneous unconstrained enhanced sampling and free energy calculations of biomolecules It works by adding a harmonic boost potential to smooth biomolecular potential energy surface and reduce energy barriers
  • OpenMM - Gaussian Accelerated Molecular Dynamics (GaMD) module
    Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calculations of biomolecules It works by adding a harmonic boost potential to smooth the potential energy surface and reduce system energy barriers http: miao compbio ku edu GaMD - MiaoLab20 gamd-openmm
  • Getting Started — game_we documentation - Read the Docs
    Gaussian accelerated molecular dynamics (GaMD) is a well-established enhanced sampling method for molecular dynamics (MD) simulations that effectively samples the potential energy landscape of the system by adding a boost potential, which smoothens the surface and lowers energy barriers between states
  • Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and . . .
    A novel Gaussian Accelerated Molecular Dynamics (GaMD) method has been developed for simultaneous unconstrained enhanced sampling and free energy calculation of biomolecules Without the need to set predefined reaction coordinates, GaMD enables unconstrained enhanced sampling of the biomolecules
  • GaMD Tutorials | Miao Lab - med. unc. edu
    Gaussian accelerated Molecular Dynamics (GaMD) is a biomolecular enhanced sampling method that works by adding a harmonic boost potential to smooth the system potential energy surface This tutorial explains how you can perform GaMD simulations using the Amber24 simulation package Alanine dipeptide is used as a model system for demonstration
  • Gaussian accelerated molecular dynamics: Principles and applications . . .
    Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for simultaneous unconstrained enhanced sampling and free energy calculations of biomolecules It works by adding a harmonic boost potential to smooth biomolecular potential energy surface and reduce energy barriers
  • An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) Multilevel . . .
    We introduce a novel multilevel enhanced sampling strategy grounded on Gaussian-accelerated Molecular Dynamics (GaMD) First, we propose a GaMD multi-GPUs-accelerated implementation within the Tinker-HP molecular dynamics package We introduce the new “dual-water” mode and its use with the flexible AMOEBA polarizable force field
  • Theory | Miao Lab - UNC School of Medicine
    Gaussian Accelerated Molecular Dynamics (GaMD) has been developed for simultaneous unconstrained enhanced sampling and free energy calculation of large biomolecules By constructing a boost potential that follows Gaussian distribution, accurate reweighting of the GaMD simulations is achieved using cumulant expansion to the second order





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