Hyperdynamics - Gaussian Accelerated Molecular Dynamics. Miao, Y. Feher, V. A. McCammon, J. A., Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation. J. Chem. Theory Comput. 2015, 11, 3584-3595. Last updated: Tue, November 22, 2016.
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Hyperdynamics - Gaussian Accelerated Molecular Dynamics (GaMD) | gamd.ucsd.edu Reviews
https://gamd.ucsd.edu
Hyperdynamics - Gaussian Accelerated Molecular Dynamics. Miao, Y. Feher, V. A. McCammon, J. A., Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation. J. Chem. Theory Comput. 2015, 11, 3584-3595. Last updated: Tue, November 22, 2016.
gamd.ucsd.edu
Hyperdynamics - Gaussian Accelerated Molecular Dynamics (GaMD)
http://gamd.ucsd.edu/index.html
Hyperdynamics - Gaussian Accelerated Molecular Dynamics. Miao, Y. Feher, V. A. McCammon, J. A., Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation. J. Chem. Theory Comput. 2015, 11, 3584-3595. Last updated: Tue, November 22, 2016.
Hyperdynamics - Gaussian Accelerated Molecular Dynamics (GaMD)
http://gamd.ucsd.edu/installation.html
Installation of GaMD in Amber. GaMD is fully supported in AMBER16, which was released on Apr 30, 2016 and can be obtained at http:/ ambermd.org. GaMD patch for Amber14. Amber14 GaMD patch confidential.txt:. GaMD patch for Amber 14 AmberTools 15. Authors: Yinglong Miao and Ross C. Walker. Date: 29th July 2015. Programs: pmemd and pmemd.cuda. Description: This patch adds temporary GaMD support to AMBER 14. It is built against AMBER 14 AmberTools 15 Amber 14 updates to 12. Ross C. Walker or Yinglong Miao.
Hyperdynamics - Gaussian Accelerated Molecular Dynamics (GaMD)
http://gamd.ucsd.edu/theory.html
Gaussian Accelerated Molecular Dynamics (GaMD) enhances the conformational sampling of biomolecules by adding a harmonic boost potential to smoothen the system potential energy surface:. Energetic Reweighting using Cumulant Expansion to the Second Order (Gaussian Approximation). Last updated: Tue, November 22, 2016.
Hyperdynamics - Gaussian Accelerated Molecular Dynamics (GaMD)
http://gamd.ucsd.edu/examples.html
Folding of chignolin was captured in GaMD simulations: the unfolded (“U”), intermediate (“I”) and folded (“F”) states (blue) aligned to the PDB native structure (red). Residues including Tyr2, Asp3, Pro4, Glu5, Thr6, Thr8 and Trp9 are represented by sticks. Notably, Trp9 and Pro4 form hydrophobic interactions in the intermediate state. Simulation Movie: chignolin-folding.mpeg. Simulation Movie: lysozyme-ligandBinding.mpeg. Simulation Movie: Movie-M2-ARC-dissociation binding.mpeg. Reference: Y. Miao a...
Hyperdynamics - Gaussian Accelerated Molecular Dynamics (GaMD)
http://gamd.ucsd.edu/manual.html
Manual of GaMD in Amber. If (irest gamd = 0) then. For i = 1, …, ntcmd / run initial conventional molecular dynamics. If (i = ntcmdprep) Update Vmax, Vmin. If (i = ntcmdprep & i%ntave = 0) Update Vavg, sigmaV. Save Vmax,Vmin,Vavg,sigmaV to “gamd restart.dat” file. Calc E k0(iE,sigma0,Vmax,Vmin,Vavg,sigmaV). For i = ntcmd 1, …, ntcmd nteb / Run biasing molecular dynamics simulation steps. DeltaV = 0.5*k0*(E-V)* 2/(Vmax-Vmin). V = V deltaV. If (i = ntcmd ntebprep) Update Vmax, Vmin. V = V deltaV. IE = 2: s...
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We have recently changed our website. Looking for the previous site? Computational Research in Molecular Chemistry. Available Through the McCammon Group:. Originated in the McCammon Group:.
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We have recently changed our website. Looking for the previous site? Computational Research in Molecular Chemistry. Available Through the McCammon Group:. Originated in the McCammon Group:.
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Hyperdynamics - Gaussian Accelerated Molecular Dynamics (GaMD)
Hyperdynamics - Gaussian Accelerated Molecular Dynamics. Miao, Y. Feher, V. A. McCammon, J. A., Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation. J. Chem. Theory Comput. 2015, 11, 3584-3595. Last updated: Tue, November 22, 2016.
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