GaMD | Miao Lab - UNC School of Medicine
网页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 (GaMD): principles …
网页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 …
网页2015年7月14日 · A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced sampling and free energy calculation of biomolecules is presented. By constructing a boost potential that follows...
An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) …
网页2022年1月26日 · 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 …
高斯加速分子动力学：原理与应用,Wiley Interdisciplinary Reviews: …
网页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: Theory, Implementation…
网页2017年1月1日 · GaMD is a novel method for enhanced sampling and free energy calculation of biomolecules without predefined reaction coordinates. It uses a harmonic function to construct a Gaussian boost potential that can be reweighted accurately using cumulant expansion to the second order.
WIREs Computational Molecular Science
网页2021年3月1日 · 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: Theory, Implementation…
网页2017年1月1日 · GaMD is a Gaussian Accelerated Molecular Dynamics technique that uses a harmonic boost potential to facilitate biomolecular conformational transitions across high-energy barriers. It does not require predefined reaction coordinates and allows for accurate reweighting of the simulations …
GaMD-Amber: Tutorial | Miao Lab - UNC School of Medicine
网页Learn how to run GaMD simulations on alanine dipeptide, LiGaMD, Pep-GaMD and PPI-GaMD_Dual using Amber software. Download PDF and source files of the tutorial and see example input parameters.
OpenMM - Gaussian Accelerated Molecular Dynamics (GaMD) …
网页GaMD-OpenMM is a Python module that implements Gaussian Accelerated Molecular Dynamics (GaMD), a method for both unconstrained enhanced sampling and free energy calculations of biomolecules. It adds a harmonic boost potential to smooth the potential energy surface and reduce system energy barriers.
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