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  Contents
- Angular Correlation (AC)
- Parameters
, Parameters
, Output
, Output
- Angular Density Of States (ADOS)
- Theory and implementation
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Output
, Output
, Output
- Angular Velocity AutoCorrelation Function (AVACF)
- Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Output
, Output
, Output
, Theory and implementation
, Analysis benchmark
- Auto-Regressive (AR)
- Theory and implementation
, Density of states within the AR model
, MSD within the AR model
, MSD within the AR model
, MSD within the AR model
, Friction coefficient within the AR model
, Friction coefficient within the AR model
, Friction coefficient within the AR model
, Friction coefficient within the AR model
, Theory and implementation
, Theory and implementation
, Theory and implementation
- Auto-Regressive Analysis (ARA)
- Theory and implementation
, Parameters
, Parameters
, Parameters
, Parameters
, Output
, Analysis benchmark
- Center Of Mass Trajectory (COMT)
- New features in version 3.0
, Theory and implementation
, Theory and implementation
, Parameters
, Parameters
, Parameters
, Output
- Chemistry at HARvard Macromolecular Mechanics (CHARMM)
- New features in version 3.0
, CHARMM/X-PLOR to MMTK
, CHARMM/X-PLOR to MMTK
, NAMD to MMTK
- Coordination Number (CN)
- New features in version 3.0
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Output
, Output
, Output
, Output
, Output
, Output
, Output
, Output
, Output
, Output
, Output
, Output
, Output
, Output
, Output
, Output
, Output
, Parameters
, Parameters
- Density Of States (DOS)
- Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Output
, Output
, Output
, Friction coefficient within the AR model
, Parameters
, Output
, Output
, Analysis benchmark
- Dynamic Coherent Structure Factor (DCSF)
- Parameters
, Parameters
, Parameters
, Output
, Analysis benchmark
- Dynamic Coherent Structure Factor using an Auto-Regressive model (DCSFAR)
- Parameters
, Parameters
, Parameters
, Output
- Dynamic Incoherent Structure Factor (DISF)
- Parameters
, Parameters
, Parameters
, Output
, Parameters
, Analysis benchmark
- Dynamic Incoherent Structure Factor using an Auto-Regressive model (DISFAR)
- Parameters
, Parameters
, Parameters
, Output
- Dynamic Incoherent Structure Factor using an Gaussian approximation (DISFG)
- Parameters
, Parameters
, Parameters
, Output
, Analysis benchmark
- Elastic Incoherent Structure Factor (EISF)
- Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Parameters
, Parameters
, Output
, Analysis benchmark
- Fast Correlation Algorithm (FCA)
- Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, The FCA algorithm
, The FCA algorithm
- Global Motion Filtered Trajectory (GMFT)
- New features in version 3.0
, Theory and implementation
, Parameters
, Parameters
, Output
- Graphical User Interface (GUI)
- Introduction
, New features in version 3.0
, New features in version 3.0
, Using nMOLDYNfrom the Graphical User Interface
, Using nMOLDYNfrom the Graphical User Interface
, Using nMOLDYNfrom the Graphical User Interface
, Using nMOLDYNfrom the Graphical User Interface
, Using nMOLDYNfrom the Graphical User Interface
, Using nMOLDYNfrom the Graphical User Interface
, Using nMOLDYNfrom the Graphical User Interface
, Running modes
, Using nMOLDYN from the command-line interface
, nMOLDYN autostart files
, nMOLDYN autostart files
, nMOLDYN input files
, nMOLDYN input files
- Mean-Square Displacement (MSD)
- Subset selection
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Parameters
, Parameters
, Parameters
, Parameters
, Output
, Output
, Output
, MSD within the AR model
, MSD within the AR model
, MSD within the AR model
, Friction coefficient within the AR model
, Parameters
, Output
, Output
, Theory and implementation
, Theory and implementation
, Analysis benchmark
, nMOLDYN autostart files
, nMOLDYN input files
- Molecular Dynamics (MD)
- nMOLDYN_for_HTML
, nMOLDYN_for_HTML
, Introduction
, Introduction
, Introduction
, Introduction
, Introduction
, Introduction
, Introduction
, Introduction
, Subset selection
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Output
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, The FCA algorithm
- Molecular Modelling ToolKit (MMTK)
- nMOLDYN_for_HTML
, nMOLDYN_for_HTML
, New features in version 3.0
, Installing nMOLDYN
, NetCDF file format
, NetCDF file format
, NetCDF file format
, NetCDF file format
, NetCDF file format
, PDB file format
, Using nMOLDYNfrom the Graphical User Interface
, Load NetCDF file
, Load NetCDF file
, Load NetCDF file
, Load NetCDF file
, Load NetCDF file
, Load NetCDF file
, Load NetCDF file
, Load NetCDF file
, Load NetCDF file
, Load NetCDF file
, Load NetCDF file
, Load NetCDF file
, Trajectory conversion
, Trajectory conversion
, Amber to MMTK
, Amber to MMTK
, Amber to MMTK
, Amber to MMTK
, Amber to MMTK
, CHARMM/X-PLOR to MMTK
, CHARMM/X-PLOR to MMTK
, CHARMM/X-PLOR to MMTK
, CHARMM/X-PLOR to MMTK
, CHARMM/X-PLOR to MMTK
, DL_POLY to MMTK
, DL_POLY to MMTK
, DL_POLY to MMTK
, DL_POLY to MMTK
, DL_POLY to MMTK
, DL_POLY to MMTK
, DL_POLY to MMTK
, Discover to MMTK
, Discover to MMTK
, Discover to MMTK
, Discover to MMTK
, Discover to MMTK
, Discover to MMTK
, Discover to MMTK
, Discover to MMTK
, Discover to MMTK
, Forcite to MMTK
, Forcite to MMTK
, Forcite to MMTK
, Forcite to MMTK
, Forcite to MMTK
, Forcite to MMTK
, Forcite to MMTK
, Forcite to MMTK
, Forcite to MMTK
, Forcite to MMTK
, NAMD to MMTK
, NAMD to MMTK
, NAMD to MMTK
, NAMD to MMTK
, NAMD to MMTK
, VASP to MMTK
, VASP to MMTK
, VASP to MMTK
, VASP to MMTK
, VASP to MMTK
, Frame snapshot
, Frame snapshot
, Convert NetCDF to ASCII
, Preferences
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, selection from the loaded trajectory
, Parameters
, Parameters
, Parameters
, Parameters
, Output
, Output
, Output
, Output
, Output
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, About nMOLDYN
- Network Common Data Form (NetCDF)
- nMOLDYN_for_HTML
, New features in version 3.0
, New features in version 3.0
, Input and output files
, Input and output files
, NetCDF file format
, NetCDF file format
, NetCDF file format
, NetCDF file format
, Using nMOLDYNfrom the Graphical User Interface
, Load NetCDF file
, Load NetCDF file
, Load NetCDF file
, Trajectory conversion
, Amber to MMTK
, Amber to MMTK
, Amber to MMTK
, Amber to MMTK
, Amber to MMTK
, Amber to MMTK
, Amber to MMTK
, Amber to MMTK
, Amber to MMTK
, Amber to MMTK
, Amber to MMTK
, CHARMM/X-PLOR to MMTK
, CHARMM/X-PLOR to MMTK
, CHARMM/X-PLOR to MMTK
, DL_POLY to MMTK
, DL_POLY to MMTK
, Discover to MMTK
, Discover to MMTK
, Discover to MMTK
, Forcite to MMTK
, Forcite to MMTK
, Forcite to MMTK
, NAMD to MMTK
, NAMD to MMTK
, NAMD to MMTK
, VASP to MMTK
, VASP to MMTK
, Frame snapshot
, Frame snapshot
, Convert NetCDF to ASCII
, Convert NetCDF to ASCII
, Convert NetCDF to ASCII
, Convert NetCDF to ASCII
, Convert NetCDF to ASCII
, Convert NetCDF to ASCII
, Convert NetCDF to ASCII
, Convert NetCDF to ASCII
, Convert NetCDF to ASCII
, Convert ASCII to NetCDF
, Convert ASCII to NetCDF
, Convert ASCII to NetCDF
, Convert ASCII to NetCDF
, Convert ASCII to NetCDF
, Convert ASCII to NetCDF
, Convert ASCII to NetCDF
, Convert ASCII to NetCDF
, Convert ASCII to NetCDF
, Preferences
, Preferences
, Preferences
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Parameters
, Output
, Parameters
, Output
, Parameters
, Output
, Parameters
, Output
, Output
, Parameters
, Output
, Parameters
, Parameters
, Parameters
, Output
, Parameters
, Output
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Output
, Parameters
, Parameters
, Output
, Plot
, Plot
, Plot
, Plot
, Plot
, Plot
, Plot
- NAnoscale Molecular Dynamics (NAMD)
- New features in version 3.0
, NAMD to MMTK
, NAMD to MMTK
- Order Parameter (OP)
- New features in version 3.0
, Parameters
, Parameters
, Output
, Output
- Order Parameter using Contact Model (OPCM)
- New features in version 3.0
, Parameters
, Parameters
, Output
, Output
- Pair-Distribution Function (PDF)
- New features in version 3.0
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Output
, Output
, Output
, Output
, Output
, Parameters
, Parameters
, Theory and implementation
, Parameters
, Parameters
- Pass-Band Filtered Trajectory (PBFT)
- Theory and implementation
, Parameters
, Parameters
, Output
- Protein Data Bank (PDB)
- PDB file format
, PDB file format
, PDB file format
, PDB file format
, nMOLDYN selection files
, Frame snapshot
, Frame snapshot
, selection from a selection file
, selection from a selection file
, selection from a selection file
, selection from a selection file
, selection from a selection file
, selection from a selection file
, selection from a selection file
- Quasi-Harmonic Analysis (QHA)
- New features in version 3.0
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Parameters
, Parameters
, Output
, Output
, Effective mode
, Effective mode
, Effective mode
, Effective mode
, Effective mode
- Radial-Distribution Function (RDF)
- Theory and implementation
, Theory and implementation
, Theory and implementation
, Parameters
, Output
, Output
, Output
, Output
- Radius Of Gyration (ROG)
- New features in version 3.0
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Parameters
, Parameters
, Parameters
, Output
, Output
, Output
- Reorientational Correlation Function (RCF)
- Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Output
, Output
, Output
- Rigid-Body Trajectory (RBT)
- Theory and implementation
, Solution of the minimization problem.
, Solution of the minimization problem.
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Output
, Output
, Output
, Output
, Parameters
, Parameters
, Parameters
- Root Mean-Square Deviation (RMSD)
- New features in version 3.0
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Parameters
, Parameters
, Parameters
, Parameters
, Output
, Output
, Output
- ScrewFit Analysis (SFA)
- Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Parameters
, Parameters
, Output
- Smoothed Static Coherent Structure Factor (SSCSF)
- New features in version 3.0
, Theory and implementation
, Parameters
, Parameters
, Parameters
, Output
- Spatial Density (SD)
- New features in version 3.0
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Output
, Output
, Output
, Output
, Output
- Static Coherent Structure Factor (SCSF)
- New features in version 3.0
, Parameters
, Parameters
, Parameters
, Output
- Total-Correlation Function (TCF)
- Theory and implementation
, Theory and implementation
, Theory and implementation
, Parameters
, Output
, Output
, Output
, Output
- University Corporation for Atmospheric Research (UCAR)
- NetCDF file format
- Velocity AutoCorrelation Function (VACF)
- Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Parameters
, Parameters
, Parameters
, Parameters
, Output
, Output
, Output
, Theory and implementation
, Theory and implementation
, Theory and implementation
, Theory and implementation
, VACF within the AR model
, VACF within the AR model
, Density of states within the AR model
, Discrete memory function of the VACF within the AR model
, MSD within the AR model
, MSD within the AR model
, Friction coefficient within the AR model
, Friction coefficient within the AR model
, Parameters
, Output
, Output
, Output
, Output
, Theory and implementation
, Analysis benchmark
- Vienna Ab-initio Simulation Package (VASP)
- New features in version 3.0
, VASP to MMTK
, VASP to MMTK
, VASP to MMTK
- Visual Molecular Dynamics (VMD)
- Animation
, Animation
, Animation
, Animation
, Animation
, Animation
, Effective mode
, Effective mode
, Effective mode
, Effective mode
, Effective mode
, Effective mode
- eXtended System Trajectory (XST)
- NAMD to MMTK
- network Common Data Language (CDL)
- Convert NetCDF to ASCII
, Convert ASCII to NetCDF
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
, Parameters
pellegrini eric
2009-10-06