Manual

• 1 Introduction
  • 1.1 About this manual
  • 1.2 Codes interfaced with PLUMED
• 2 Change Log
  • 2.1 Version 2.0
  • 2.2 Version 2.1
  • 2.3 Version 2.2
  • 2.4 Version 2.3
  • 2.5 Version 2.4
  • 2.6 Unreleased changes
• 3 Installation
  • 3.1 Supported compilers
  • 3.2 Configuring PLUMED
    • 3.2.1 BLAS and LAPACK
    • 3.2.2 VMD trajectory plugins
  • 3.3 Compiling PLUMED
  • 3.4 Installing PLUMED
  • 3.5 Patching your MD code
  • 3.6 Cross compiling
  • 3.7 Installing PLUMED with MacPorts
  • 3.8 Installing PLUMED on a cluster
  • 3.9 Other hints
  • 3.10 Code specific notes
    • 3.10.1 amber14
    • 3.10.2 gromacs-2016.4
    • 3.10.3 gromacs-4.5.7
    • 3.10.4 gromacs-5.1.4
    • 3.10.5 lammps-6Apr13
    • 3.10.6 namd-2.8
    • 3.10.7 namd-2.9
    • 3.10.8 qespresso-5.0.2
    • 3.10.9 qespresso-6.2
• 4 Getting Started
  • 4.1 Plumed units
  • 4.2 UNITS
• 5 Collective Variables
  • 5.1 Groups and Virtual Atoms
    • 5.1.1 Specifying Atoms
      • 5.1.1.1 Molecules
      • 5.1.1.2 Broken Molecules and PBC
    • 5.1.2 Virtual Atoms
    • 5.1.3 GROUP
    • 5.1.4 MOLINFO
    • 5.1.5 WHOLEMOLECULES
    • 5.1.6 FIT_TO_TEMPLATE
    • 5.1.7 WRAPAROUND
    • 5.1.8 RESET_CELL
    • 5.1.9 CENTER_OF_MULTICOLVAR
    • 5.1.10 CENTER
    • 5.1.11 COM
    • 5.1.12 FIXEDATOM
    • 5.1.13 GHOST
  • 5.2 CV Documentation
    • 5.2.1 ADAPTIVE_PATH
    • 5.2.2 ALPHABETA
    • 5.2.3 ALPHARMSD
    • 5.2.4 ANGLE
    • 5.2.5 ANTIBETARMSD
    • 5.2.6 CELL
    • 5.2.7 CONSTANT
    • 5.2.8 CONTACTMAP
    • 5.2.9 COORDINATION
    • 5.2.10 DHENERGY
    • 5.2.11 DIHCOR
    • 5.2.12 DIMER
    • 5.2.13 DIPOLE
    • 5.2.14 DISTANCE_FROM_CONTOUR
    • 5.2.15 DISTANCE
    • 5.2.16 EEFSOLV
    • 5.2.17 ENERGY
    • 5.2.18 ERMSD
    • 5.2.19 FAKE
    • 5.2.20 GPROPERTYMAP
    • 5.2.21 GYRATION
    • 5.2.22 PARABETARMSD
    • 5.2.23 PATHMSD
    • 5.2.24 PATH
    • 5.2.25 PCAVARS
    • 5.2.26 POSITION
    • 5.2.27 PROPERTYMAP
    • 5.2.28 PUCKERING
    • 5.2.29 TEMPLATE
    • 5.2.30 TORSION
    • 5.2.31 VOLUME
  • 5.3 Distances from reference configurations
    • 5.3.1 DRMSD
    • 5.3.2 MULTI-RMSD
    • 5.3.3 PCARMSD
    • 5.3.4 RMSD
    • 5.3.5 TARGET
  • 5.4 Functions
    • 5.4.1 COMBINE
    • 5.4.2 CUSTOM
    • 5.4.3 ENSEMBLE
    • 5.4.4 FUNCPATHMSD
    • 5.4.5 FUNCSUMHILLS
    • 5.4.6 LOCALENSEMBLE
    • 5.4.7 MATHEVAL
      • 5.4.7.1 TIME
    • 5.4.8 PIECEWISE
    • 5.4.9 SORT
    • 5.4.10 STATS
  • 5.5 MultiColvar
    • 5.5.1 MultiColvar functions
    • 5.5.2 MultiColvar bias
    • 5.5.3 ANGLES
    • 5.5.4 BOND_DIRECTIONS
    • 5.5.5 BRIDGE
    • 5.5.6 COORDINATIONNUMBER
    • 5.5.7 DENSITY
    • 5.5.8 DISTANCES
    • 5.5.9 FCCUBIC
    • 5.5.10 HBPAMM_SH
    • 5.5.11 INPLANEDISTANCES
    • 5.5.12 MOLECULES
    • 5.5.13 PLANES
    • 5.5.14 Q3
    • 5.5.15 Q4
    • 5.5.16 Q6
    • 5.5.17 SIMPLECUBIC
    • 5.5.18 TETRAHEDRAL
    • 5.5.19 TORSIONS
    • 5.5.20 XANGLES
    • 5.5.21 XDISTANCES
    • 5.5.22 XYDISTANCES
    • 5.5.23 XYTORSIONS
    • 5.5.24 XZDISTANCES
    • 5.5.25 XZTORSIONS
    • 5.5.26 YANGLES
    • 5.5.27 YDISTANCES
    • 5.5.28 YXTORSIONS
    • 5.5.29 YZDISTANCES
    • 5.5.30 YZTORSIONS
    • 5.5.31 ZANGLES
    • 5.5.32 ZDISTANCES
    • 5.5.33 ZXTORSIONS
    • 5.5.34 ZYTORSIONS
    • 5.5.35 MFILTER_BETWEEN
    • 5.5.36 MFILTER_LESS
    • 5.5.37 MFILTER_MORE
    • 5.5.38 AROUND
    • 5.5.39 CAVITY
    • 5.5.40 INCYLINDER
    • 5.5.41 INENVELOPE
    • 5.5.42 INSPHERE
    • 5.5.43 TETRAHEDRALPORE
    • 5.5.44 GRADIENT
    • 5.5.45 INTERMOLECULARTORSIONS
    • 5.5.46 LOCAL_AVERAGE
    • 5.5.47 LOCAL_Q3
    • 5.5.48 LOCAL_Q4
    • 5.5.49 LOCAL_Q6
    • 5.5.50 MCOLV_COMBINE
    • 5.5.51 MCOLV_PRODUCT
    • 5.5.52 NLINKS
    • 5.5.53 PAMM
    • 5.5.54 POLYMER_ANGLES
    • 5.5.55 SMAC
    • 5.5.56 MTRANSFORM_BETWEEN
    • 5.5.57 MTRANSFORM_LESS
    • 5.5.58 MTRANSFORM_MORE
    • 5.5.59 LWALLS
    • 5.5.60 UWALLS
  • 5.6 Exploiting contact matrices
    • 5.6.1 ALIGNED_MATRIX
    • 5.6.2 CONTACT_MATRIX
    • 5.6.3 HBOND_MATRIX
    • 5.6.4 HBPAMM_MATRIX
    • 5.6.5 SMAC_MATRIX
    • 5.6.6 TOPOLOGY_MATRIX
    • 5.6.7 CLUSTER_WITHSURFACE
    • 5.6.8 COLUMNSUMS
    • 5.6.9 DFSCLUSTERING
    • 5.6.10 ROWSUMS
    • 5.6.11 SPRINT
    • 5.6.12 CLUSTER_DIAMETER
    • 5.6.13 CLUSTER_DISTRIBUTION
    • 5.6.14 CLUSTER_NATOMS
    • 5.6.15 CLUSTER_PROPERTIES
    • 5.6.16 DUMPGRAPH
    • 5.6.17 OUTPUT_CLUSTER
• 6 Analysis
  • 6.1 Dimensionality Reduction
  • 6.2 COMMITTOR
  • 6.3 DUMPATOMS
  • 6.4 DUMPDERIVATIVES
  • 6.5 DUMPFORCES
  • 6.6 DUMPMASSCHARGE
  • 6.7 DUMPMULTICOLVAR
  • 6.8 DUMPPROJECTIONS
  • 6.9 PRINT
    • 6.9.1 FLUSH
  • 6.10 UPDATE_IF
  • 6.11 REWEIGHT_BIAS
  • 6.12 REWEIGHT_METAD
  • 6.13 REWEIGHT_TEMP
  • 6.14 AVERAGE
  • 6.15 HISTOGRAM
  • 6.16 MULTICOLVARDENS
  • 6.17 CONVERT_TO_FES
  • 6.18 DUMPCUBE
  • 6.19 DUMPGRID
  • 6.20 FIND_CONTOUR_SURFACE
  • 6.21 FIND_CONTOUR
  • 6.22 FIND_SPHERICAL_CONTOUR
  • 6.23 FOURIER_TRANSFORM
  • 6.24 GRID_TO_XYZ
  • 6.25 INTEGRATE_GRID
  • 6.26 INTERPOLATE_GRID
  • 6.27 CLASSICAL_MDS
    • 6.27.1 Method of optimisation
  • 6.28 PCA
• 7 Bias
  • 7.1 ABMD
  • 7.2 BIASVALUE
  • 7.3 EXTENDED_LAGRANGIAN
  • 7.4 EXTERNAL
  • 7.5 LOWER_WALLS
  • 7.6 MAXENT
  • 7.7 METAD
  • 7.8 MOVINGRESTRAINT
  • 7.9 PBMETAD
  • 7.10 RESTRAINT
  • 7.11 UPPER_WALLS
  • 7.12 RESTART
• 8 Additional Modules
  • 8.1 PLUMED-ISDB
    • 8.1.1 CVs Documentation
      • 8.1.1.1 CS2BACKBONE
      • 8.1.1.2 EMMI
      • 8.1.1.3 FRET
      • 8.1.1.4 JCOUPLING
      • 8.1.1.5 NOE
      • 8.1.1.6 PCS
      • 8.1.1.7 PRE
      • 8.1.1.8 RDC
      • 8.1.1.9 SAXS
    • 8.1.2 Functions Documentation
      • 8.1.2.1 SELECT
    • 8.1.3 Biases Documentation
      • 8.1.3.1 METAINFERENCE
      • 8.1.3.2 RESCALE
    • 8.1.4 SELECTOR
    • 8.1.5 Tutorials
      • 8.1.5.1 ISDB: setting up a Metadynamic Metainference simulation
  • 8.2 Experiment Directed Simulation
    • 8.2.1 Biases Documentation
      • 8.2.1.1 EDS
  • 8.3 Extended-System Adaptive Biasing Force
    • 8.3.1 Biases Documentation
      • 8.3.1.1 DRR
    • 8.3.2 Command Line Tools
      • 8.3.2.1 drr_tool
  • 8.4 Variationally Enhanced Sampling (VES code)
    • 8.4.1 Biases
      • 8.4.1.1 VES_LINEAR_EXPANSION
    • 8.4.2 Basis functions
      • 8.4.2.1 BF_CHEBYSHEV
      • 8.4.2.2 BF_COMBINED
      • 8.4.2.3 BF_COSINE
      • 8.4.2.4 BF_CUSTOM
      • 8.4.2.5 BF_FOURIER
      • 8.4.2.6 BF_LEGENDRE
      • 8.4.2.7 BF_POWERS
      • 8.4.2.8 BF_SINE
    • 8.4.3 Target Distributions
      • 8.4.3.1 TD_CHISQUARED
      • 8.4.3.2 TD_CHI
      • 8.4.3.3 TD_CUSTOM
      • 8.4.3.4 TD_EXPONENTIALLY_MODIFIED_GAUSSIAN
      • 8.4.3.5 TD_EXPONENTIAL
      • 8.4.3.6 TD_GAUSSIAN
      • 8.4.3.7 TD_GENERALIZED_EXTREME_VALUE
      • 8.4.3.8 TD_GENERALIZED_NORMAL
      • 8.4.3.9 TD_GRID
      • 8.4.3.10 TD_LINEAR_COMBINATION
      • 8.4.3.11 TD_PRODUCT_COMBINATION
      • 8.4.3.12 TD_PRODUCT_DISTRIBUTION
      • 8.4.3.13 TD_UNIFORM
      • 8.4.3.14 TD_VONMISES
      • 8.4.3.15 TD_WELLTEMPERED
    • 8.4.4 Optimizers
      • 8.4.4.1 OPT_AVERAGED_SGD
      • 8.4.4.2 OPT_DUMMY
    • 8.4.5 Utilities
      • 8.4.5.1 VES_OUTPUT_BASISFUNCTIONS
      • 8.4.5.2 VES_OUTPUT_FES
      • 8.4.5.3 VES_OUTPUT_TARGET_DISTRIBUTION
    • 8.4.6 Command Line Tools
      • 8.4.6.1 ves_md_linearexpansion
    • 8.4.7 Tutorials
      • 8.4.7.1 MARVEL-VES School February 2017
      • 8.4.7.2 MARVEL-VES tutorial (Lugano Feb 2017): Metadynamics
      • 8.4.7.3 MARVEL-VES tutorial (Lugano Feb 2017): VES 1
      • 8.4.7.4 MARVEL-VES tutorial (Lugano Feb 2017): VES 2
      • 8.4.7.5 MARVEL-VES tutorial (Lugano Feb 2017): Kinetics
• 9 Command Line Tools
  • 9.1 driver-float
  • 9.2 driver
    • 9.2.1 READ
  • 9.3 gentemplate
  • 9.4 info
  • 9.5 kt
  • 9.6 manual
  • 9.7 pathtools
  • 9.8 pesmd
  • 9.9 simplemd
  • 9.10 sum_hills
• 10 Miscelaneous
  • 10.1 Comments
    • 10.1.1 ENDPLUMED
  • 10.2 Continuation lines
  • 10.3 Using VIM syntax file
  • 10.4 Including other files
    • 10.4.1 INCLUDE
  • 10.5 Loading shared libraries
    • 10.5.1 LOAD
  • 10.6 Debugging the code
    • 10.6.1 DEBUG
  • 10.7 Changing exchange patterns in replica exchange
    • 10.7.1 RANDOM_EXCHANGES
  • 10.8 List of modules
  • 10.9 Special replica syntax
  • 10.10 Parsing constants
  • 10.11 Frequently used tools
    • 10.11.1 histogrambead
    • 10.11.2 kernelfunctions
    • 10.11.3 landmarkselection
    • 10.11.4 pdbreader
    • 10.11.5 switchingfunction
    • 10.11.6 Regular Expressions
    • 10.11.7 Files
      • 10.11.7.1 Restart
      • 10.11.7.2 Backup
      • 10.11.7.3 Replica suffix
• 11 Tutorials
  • 11.1 Trieste tutorial: Analyzing trajectories using PLUMED
    • 11.1.1 Aims
    • 11.1.2 Objectives
    • 11.1.3 Resources
    • 11.1.4 Introduction
    • 11.1.5 Using PLUMED from the command line
    • 11.1.6 The structure of a PLUMED input file
      • 11.1.6.1 Exercise 1: Computing and printing collective variables
      • 11.1.6.2 Exercise 1b: Combining collective variables
    • 11.1.7 Solving periodic-boundary conditions issues
      • 11.1.7.1 Exercise 2: Solving PBC issues and dump atomic coordinates
      • 11.1.7.2 Exercise 2b: Mistakes with WHOLEMOLECULES
      • 11.1.7.3 Exercise 2c: Mastering FIT_TO_TEMPLATE
      • 11.1.7.4 Conclusions
  • 11.2 Trieste tutorial: Averaging, histograms and block analysis
    • 11.2.1 Introduction
    • 11.2.2 Objectives
    • 11.2.3 Background
    • 11.2.4 Instructions
      • 11.2.4.1 Calculating an ensemble average
      • 11.2.4.2 Calculating a histogram
      • 11.2.4.3 Problem I: Making the best use of the data
      • 11.2.4.4 Problem II: Dealing with rare events and simulation biases
      • 11.2.4.5 Problem III: Dealing with correlated variables
      • 11.2.4.6 Putting it all together
    • 11.2.5 Extensions
  • 11.3 Trieste tutorial: Using restraints
    • 11.3.1 Aims
    • 11.3.2 Objectives
    • 11.3.3 Resources
    • 11.3.4 Introduction
      • 11.3.4.1 Biased sampling
    • 11.3.5 Exercise 1: converged histogram of the water dimer relative distance
    • 11.3.6 Exercise 2: Apply a linear restraint on the same collective variable
    • 11.3.7 Exercise 3: Apply a quadratic restraint on the same collective variable
    • 11.3.8 Exercise 4: Apply an upper wall on the distance.
    • 11.3.9 Exercise 5: Evaluate the free energy and use it as an external restraint
    • 11.3.10 Exercise 6: Preliminary run with Alanine dipeptide
    • 11.3.11 Exercise 7: First biased run with Alanine dipeptide
    • 11.3.12 Exercise 8: Second biased run with Alanine dipeptide
  • 11.4 Trieste tutorial: Metadynamics simulations with PLUMED
    • 11.4.1 Aims
    • 11.4.2 Objectives
    • 11.4.3 Resources
    • 11.4.4 Introduction
    • 11.4.5 Exercise 1: my first metadynamics calculation
      • 11.4.5.1 Exercise 1a: setup and run
      • 11.4.5.2 Exercise 1b: estimating the free energy
    • 11.4.6 Exercise 2: playing with collective variables
    • 11.4.7 Exercise 3: estimating the error in free-energies using block-analysis
    • 11.4.8 Conclusions
  • 11.5 Trieste tutorial: Running and analyzing multi-replica simulations.
    • 11.5.1 Aims
    • 11.5.2 Objectives
    • 11.5.3 Resources
    • 11.5.4 Introduction
    • 11.5.5 Multi replica input files
    • 11.5.6 Using special syntax for multiple replicas
    • 11.5.7 Exercise 1: Running multi-replica simulations
    • 11.5.8 Exercise 2: Analyzing a multiple-restraint simulation
    • 11.5.9 Exercise 3: What if a variable is missing?
    • 11.5.10 Exercise 4: `¨demuxing`¨ your trajectories
    • 11.5.11 Conclusions
  • 11.6 Trieste tutorial: Real-life applications with complex CVs
    • 11.6.1 Aims
    • 11.6.2 Objectives
    • 11.6.3 Resources
    • 11.6.4 Introduction
    • 11.6.5 Exercise 1: analysis of the BARD1 complex simulation
    • 11.6.6 Exercise 2: analysis of the cmyc-urea simulation
    • 11.6.7 Exercise 3: Protein G folding simulations
    • 11.6.8 Conclusions
  • 11.7 Belfast tutorial: Analyzing CVs
    • 11.7.1 Aims
    • 11.7.2 Learning Outcomes
    • 11.7.3 Resources
    • 11.7.4 Instructions
      • 11.7.4.1 A note on units
      • 11.7.4.2 Introduction to the PLUMED input file
      • 11.7.4.3 MULTICOLVAR
      • 11.7.4.4 Analysis of Collective Variables
  • 11.8 Belfast tutorial: Adaptive variables I
    • 11.8.1 Aim
    • 11.8.2 Resources
    • 11.8.3 What happens when in a complex reaction?
    • 11.8.4 Path collective variables
    • 11.8.5 A note on the path topology
    • 11.8.6 How many frames do I need?
    • 11.8.7 Some tricks of the trade: the neighbors list.
    • 11.8.8 The molecule of the day: alanine dipeptide
    • 11.8.9 Examples
    • 11.8.10 How to format my input?
    • 11.8.11 Fast forward: metadynamics on the path
  • 11.9 Belfast tutorial: Adaptive variables II
    • 11.9.1 Aims
    • 11.9.2 Learning Outcomes
    • 11.9.3 Resources
    • 11.9.4 Instructions
      • 11.9.4.1 Visualising the trajectory
      • 11.9.4.2 Installing GISMO
      • 11.9.4.3 Finding collective variables
      • 11.9.4.4 Dimensionality reduction
    • 11.9.5 Extensions
    • 11.9.6 Further Reading
  • 11.10 Belfast tutorial: Umbrella sampling
    • 11.10.1 Aims
    • 11.10.2 Summary of theory
      • 11.10.2.1 Biased sampling
      • 11.10.2.2 Umbrella sampling
      • 11.10.2.3 Weighted histogram analysis method
    • 11.10.3 Learning Outcomes
    • 11.10.4 Resources
    • 11.10.5 Instructions
      • 11.10.5.1 The model system
      • 11.10.5.2 Restrained simulations
      • 11.10.5.3 Reweighting the results
      • 11.10.5.4 A free-energy landscape
      • 11.10.5.5 Combining multiple restraints
    • 11.10.6 Comments
      • 11.10.6.1 How does PLUMED work
    • 11.10.7 Further Reading
  • 11.11 Belfast tutorial: Out of equilibrium dynamics
    • 11.11.1 Resources
    • 11.11.2 Steered MD
    • 11.11.3 Moving on a more complex path
    • 11.11.4 Why work is important?
    • 11.11.5 Targeted MD
  • 11.12 Belfast tutorial: Metadynamics
    • 11.12.1 Aims
    • 11.12.2 Summary of theory
    • 11.12.3 Learning Outcomes
    • 11.12.4 Resources
    • 11.12.5 Instructions
      • 11.12.5.1 The model system
      • 11.12.5.2 Exercise 1. Setup and run a metadynamics simulation
      • 11.12.5.3 Exercise 2. Restart a metadynamics simulation
      • 11.12.5.4 Exercise 3. Calculate free-energies and monitor convergence
      • 11.12.5.5 Exercise 4. Setup and run a well-tempered metadynamics simulation, part I
      • 11.12.5.6 Exercise 5. Setup and run a well-tempered metadynamics simulation, part II
  • 11.13 Belfast tutorial: Replica exchange I
    • 11.13.1 Aims
    • 11.13.2 Summary of theory
    • 11.13.3 Learning Outcomes
    • 11.13.4 Resources
    • 11.13.5 Instructions
      • 11.13.5.1 The model system
      • 11.13.5.2 Exercise 1. Setup and run a PT simulation, part I
      • 11.13.5.3 Exercise 2. Setup and run a PT simulation, part II
      • 11.13.5.4 Exercise 3. Setup and run a PTMetaD simulation
      • 11.13.5.5 Exercise 4. The Well-Tempered Ensemble
  • 11.14 Belfast tutorial: Replica exchange II and Multiple walkers
    • 11.14.1 Aims
      • 11.14.1.1 Learning Outcomes
    • 11.14.2 Resources
    • 11.14.3 Instructions
      • 11.14.3.1 Bias-Exchange Metadynamics
      • 11.14.3.2 Convergence of the Simulations
      • 11.14.3.3 Bias-Exchange Analysis with METAGUI
      • 11.14.3.4 Multiple Walker Metadynamics
    • 11.14.4 Reference
  • 11.15 Belfast tutorial: NMR restraints
    • 11.15.1 Aims
      • 11.15.1.1 Learning Outcomes
    • 11.15.2 Resources
    • 11.15.3 Instructions
      • 11.15.3.1 Experimental data as Collective Variables
      • 11.15.3.2 Replica-Averaged Restrained Simulations
    • 11.15.4 Reference
  • 11.16 Belfast tutorial: Steinhardt Parameters
    • 11.16.1 Aims
      • 11.16.1.1 Learning Outcomes
    • 11.16.2 Resources
    • 11.16.3 Instructions
      • 11.16.3.1 Simplemd
      • 11.16.3.2 Coordination Numbers
      • 11.16.3.3 Steinhard parameter
      • 11.16.3.4 Local versus Global
      • 11.16.3.5 Local Steinhardt parameters
    • 11.16.4 Further Reading
  • 11.17 Cambridge tutorial
    • 11.17.1 Alanine dipeptide: our toy model
    • 11.17.2 Exercise 1. Metadynamics
      • 11.17.2.1 Resources
      • 11.17.2.2 Summary of theory
      • 11.17.2.3 Setup, run, and analyse a well-tempered metadynamics simulation
      • 11.17.2.4 Calculate free-energies and monitor convergence
    • 11.17.3 Exercise 2. Bias-Exchange Metadynamics
      • 11.17.3.1 Resources
      • 11.17.3.2 Summary of theory
      • 11.17.3.3 Setup, run, and analyse a well-tempered bias-exchange metadynamics simulation
      • 11.17.3.4 Calculate free-energies and monitor convergence
    • 11.17.4 Exercise 3. Replica-Average Metadynamics
      • 11.17.4.1 Resources
      • 11.17.4.2 Summary of theory
      • 11.17.4.3 The system: Chignolin
      • 11.17.4.4 Setup, run and analysis
  • 11.18 Cineca tutorial
    • 11.18.1 Resources
    • 11.18.2 Alanine dipeptide: our toy model
    • 11.18.3 Monitoring collective variables
      • 11.18.3.1 Exercise 1: on-the-fly analysis
      • 11.18.3.2 Exercise 2: analysis with the driver tool
    • 11.18.4 Biasing collective variables
      • 11.18.4.1 Metadynamics
      • 11.18.4.2 Restraints
      • 11.18.4.3 Using multiple replicas
      • 11.18.4.4 Using multiple restraints with replica exchange
  • 11.19 Using Hamiltonian replica exchange with GROMACS
    • 11.19.1 Generate scaled topologies
    • 11.19.2 Run GROMACS
  • 11.20 Julich tutorial: Developing CVs in plumed
    • 11.20.1 Aims
    • 11.20.2 Learning Outcomes
    • 11.20.3 Resources
    • 11.20.4 Introduction
    • 11.20.5 Instructions
      • 11.20.5.1 Calculating a reasonably complex collective variable
      • 11.20.5.2 Implementing a new collective variable
    • 11.20.6 Final thoughts
  • 11.21 Lugano tutorial: Analyzing CVs
    • 11.21.1 Aims
    • 11.21.2 Learning Outcomes
    • 11.21.3 Resources
    • 11.21.4 Instructions
      • 11.21.4.1 PLUMED2's internal units
      • 11.21.4.2 Introduction to the PLUMED input file
      • 11.21.4.3 The PLUMED input syntax
      • 11.21.4.4 Center of mass positions
      • 11.21.4.5 Calculating torsions
      • 11.21.4.6 An exercise with the radius of gyration
      • 11.21.4.7 Coordination numbers
      • 11.21.4.8 Multicolvar
      • 11.21.4.9 Understanding the need for ensemble averages
      • 11.21.4.10 Calculating ensemble averages using PLUMED
      • 11.21.4.11 Calculating histograms
      • 11.21.4.12 A histogram for the protein trajectory
    • 11.21.5 Conclusions and further work
  • 11.22 Lugano tutorial: Path CVs
    • 11.22.1 Aims
    • 11.22.2 Learning Outcomes
    • 11.22.3 Resources
    • 11.22.4 Instructions
      • 11.22.4.1 PCA coordinates
      • 11.22.4.2 PCA with the RMSD metric
      • 11.22.4.3 The isocommitor surface
      • 11.22.4.4 Path collective variables
      • 11.22.4.5 The mathematics of path collective variables
      • 11.22.4.6 The Z(X) collective variable
      • 11.22.4.7 Optimising path collective variables
    • 11.22.5 Conclusions and further work
  • 11.23 Moving from PLUMED 1 to PLUMED 2
    • 11.23.1 New syntax
    • 11.23.2 Groups
    • 11.23.3 Names in output files
    • 11.23.4 Units
    • 11.23.5 Directives
  • 11.24 Munster tutorial
    • 11.24.1 Alanine dipeptide: our toy model
    • 11.24.2 Monitoring collective variables
      • 11.24.2.1 Analyze on the fly
      • 11.24.2.2 Analyze using the driver
      • 11.24.2.3 Periodic boundaries and explicit water
      • 11.24.2.4 Other analysis tools
    • 11.24.3 Biasing collective variables
      • 11.24.3.1 Metadynamics
      • 11.24.3.2 Restraints
      • 11.24.3.3 Moving restraints
      • 11.24.3.4 Using multiple replicas
      • 11.24.3.5 Using multiple restraints with replica exchange
• 12 Performances
  • 12.1 GROMACS and PLUMED with GPU
  • 12.2 Metadynamics
  • 12.3 Multiple time stepping
    • 12.3.1 EFFECTIVE_ENERGY_DRIFT
  • 12.4 Multicolvar
  • 12.5 Neighbour Lists
  • 12.6 OpenMP
  • 12.7 Secondary Structure
  • 12.8 Time your Input
• 13 Index of Actions
  • 13.1 Full list of actions
• 14 Bug List
• Bibliography