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List of Acronyms

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