Browse the lessons

The lessons that have been submitted to the PLUMED-TUTORIALS are listed below. PLUMED-TUTORIAL monitors whether PLUMED input files in these lessons are compatible with the current and development versions of the code and integrates links from these files to the PLUMED manual. Inputs in the tutorials listed below were last tested on .

ID Name Instructors Description Actions Modules
23.004 Rewriting the coordination for plumed in Cuda Rapetti D. How I reimplemented a basic version of the CV Coordination with cuda    
23.002 Introduction to the plumed parallel features avaiable to the developers Rapetti D. A simple presentation of some of the avaiable features in plumed to simplify the interface with OpenMP and MPI. The lesson contains also a very simple example in how to implement a cuda CV.    
22.013 SASA module - The solvent accessible surface area of proteins as a collective variable, and the application of PLUMED for implicit solvent simulations Arsiccio A. An introduction to the SASA module and a description of how PLUMED can be used for implicit solvent simulations. LOWEST SECONDARY_STRUCTURE_RMSD GYRATION BIASVALUE ANTIBETARMSD SUM PRINT MOLINFO SASA_HASEL LESS_THAN ALPHARMSD PARABETARMSD generic colvar bias function secondarystructure sasa
22.010 Hamiltonian replica exchange with PLUMED and GROMACS Bussi G. An introduction to running Hamiltonian replica exchange calculations using PLUMED and GROMACS. MOLINFO PRINT TORSION generic colvar
22.007 Learning and enhancing fluctuations along information bottleneck for automated enhanced sampling Tiwary P. An introduction to the state predictive information bottleneck (SPIB) deep-learning-based framework for learning reaction coordinates from high dimensional molecular simulation trajectories.    
22.003 Rethinking Metadynamics using the OPES method Invernizzi M. An introduction to the On-the-fly Probability Enhanced Sampling method ENERGY ECV_UMBRELLAS_LINE OPES_METAD_EXPLORE ECV_MULTITHERMAL OPES_METAD OPES_EXPANDED TORSION colvar opes
21.007 Optimizing PLUMED performances Bonomi M. Some lessons on monitoring and improving the performance of PLUMED and gromacs EFFECTIVE_ENERGY_DRIFT GROUP METAD RMSD COORDINATION PRINT DISTANCE WHOLEMOLECULES COMBINE CUSTOM DEBUG generic colvar bias core function
21.005 Replica exchange methods Bussi G. Runninge umbrella sampling with replica exchange, bias exchange metadynamics and parallel tempering metadynamics RANDOM_EXCHANGES METAD RESTRAINT PRINT MOLINFO TORSION generic colvar bias
21.003 Umbrella Sampling Bussi G. How to calculate statistical averages and free energy surfaces using umbrella sampling HISTOGRAM BIASVALUE PRINT RESTRAINT DUMPGRID MOLINFO READ CUSTOM CONVERT_TO_FES TORSION REWEIGHT_BIAS generic colvar bias gridtools function
21.001 PLUMED syntax and analysis Bonomi M. Basic features of the PLUMED input syntax with a particular focus on PBCs and selection tools CENTER GYRATION PARABETARMSD ANTIBETARMSD DUMPATOMS PRINT DISTANCE WHOLEMOLECULES MOLINFO COMBINE ALPHARMSD TORSION generic colvar vatom function secondarystructure
23.003 Profiling, GPUs and PLUMED Bhardwaj K. A report based on some profiling work on PLUMED that has been performed by the SSEC    
23.001 Developments in PLUMED Tribello G. A series of articles were I outline some development work that I have been doing with PLUMED over the last few years PDB2CONSTANT RMSD RESTRAINT DISTANCE_MATRIX REFERENCE_GRID COMBINE GSYMFUNC_THREEBODY VOLUME LOCAL_Q1 RDF DIFFERENCE OUTER_PRODUCT HISTOGRAM INSPHERE PATH PAIRENTROPY CLUSTER_WEIGHTS FIXEDATOM CONTACT_MATRIX AVERAGE MORE_THAN LOCAL_AVERAGE VSTACK CENTER RMSD_VECTOR MATRIX_PRODUCT DUMPGRID SPRINT EUCLIDEAN_DISTANCE MATRIX_VECTOR_PRODUCT SUM ACCUMULATE CONSTANT DIAGONALIZE MEAN PRINT DISTANCE TORSION ONES KDE Q4 INTEGRATE_GRID COORDINATIONNUMBER POSITION GATHER_REPLICAS DFSCLUSTERING Q1 CONCATENATE BIASVALUE GEOMETRIC_PATH TRANSPOSE LESS_THAN SELECT_COMPONENTS SPHERICAL_HARMONIC DISPLACEMENT CUSTOM SORT Q6 WHOLEMOLECULES LOWEST GPATH INTERPOLATE_GRID COM DISTANCES GROUP DOMAIN_DECOMPOSITION PCAVARS CLUSTER_PROPERTIES colvar function volumes multicolvar adjmat clusters mapping core generic symfunc bias valtools gridtools refdist vatom sprint matrixtools
22.012 Free energy calculations in crystalline solids Piaggi P. An introduction to the Environmental similarity CV and the calculation of chemical potentials of liquids and solids LOWER_WALLS ONES CUSTOM Q6 MATHEVAL DISTANCE_MATRIX MORE_THAN DUMPGRID ENVIRONMENTSIMILARITY MATRIX_VECTOR_PRODUCT GROUP UPPER_WALLS SUM OPES_METAD HISTOGRAM MEAN function core adjmat envsim symfunc generic opes bias gridtools matrixtools
22.008 Modelling Concentration-driven processes with PLUMED Salvalaglio M. An introduction to the tools that are available in PLUMED for simulating concentration-driven processes such as nucleation, growth and diffusion. PRINT CONTACT_MATRIX FLUSH ONES RESTRAINT MORE_THAN COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT GROUP SUM DFSCLUSTERING CLUSTER_DISTRIBUTION CLUSTER_NATOMS MEAN function core adjmat clusters symfunc generic bias matrixtools
22.005 Machine learning collective variables with PyTorch Bonati L. An introduction to designing data-driven CVs using two methods (DeepLDA and DeepTICA). PRINT PYTORCH_MODEL TORSION colvar generic pytorch
22.002 Analysis of Plumed output by Metadynminer Spiwok V. An introduction to the R package Metadynminer which can be used to analyse the output from metadynamics simulatiosn    
21.006 Dimensionality reduction Tribello G. An introduction to tehcniques such as dimensionality reduction, path collective variables and indistinguishablity that you may need to use in your own research projects RMSD CLASSICAL_MDS SKETCHMAP HISTOGRAM PATH DUMPPDB UNITS MORE_THAN DUMPGRID TORSION PCA PRINT FCCUBIC DUMPVECTOR COORDINATIONNUMBER LANDMARK_SELECT_FPS PARABETARMSD DUMPMULTICOLVAR PROJECT_POINTS COMMITTOR ALPHARMSD MOLINFO ANTIBETARMSD GROUP COLLECT_FRAMES PCAVARS colvar function multicolvar dimred core mapping generic symfunc setup landmarks gridtools secondarystructure
21.004 Metadynamics Bonomi M. How to calculate statistical averages and free energy surfaces using metadynamics PRINT REWEIGHT_BIAS DUMPGRID CONVERT_TO_FES MOLINFO METAD HISTOGRAM TORSION colvar generic gridtools bias
21.002 Statistical errors in MD Tribello G. How to calculate errors on averages calculated from unbiased and biased MD simulations using the method of block averages. PRINT UNITS AVERAGE CUSTOM REWEIGHT_BIAS DISTANCE RESTRAINT COORDINATIONNUMBER READ DUMPGRID CONVERT_TO_FES COM UPPER_WALLS METAD HISTOGRAM CONSTANT colvar function generic symfunc bias setup gridtools vatom
20.001 Installing PLUMED Tribello G. An interactive tutorial resource on compiling PLUMED and linking it with MD codes.