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.

ID Name Instructors Description Actions
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. SASA_HASEL ALPHARMSD PRINT PARABETARMSD MOLINFO BIASVALUE GYRATION ANTIBETARMSD
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
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 ECV_MULTITHERMAL OPES_METAD_EXPLORE OPES_EXPANDED ENERGY TORSION OPES_METAD ECV_UMBRELLAS_LINE
21.007 Optimizing PLUMED performances Bonomi M. Some lessons on monitoring and improving the performance of PLUMED and gromacs DEBUG COMBINE WHOLEMOLECULES CUSTOM PRINT COORDINATION RMSD DISTANCE GROUP METAD EFFECTIVE_ENERGY_DRIFT
21.005 Replica exchange methods Bussi G. Runninge umbrella sampling with replica exchange, bias exchange metadynamics and parallel tempering metadynamics RANDOM_EXCHANGES PRINT MOLINFO TORSION METAD RESTRAINT
21.003 Umbrella Sampling Bussi G. How to calculate statistical averages and free energy surfaces using umbrella sampling CUSTOM HISTOGRAM CONVERT_TO_FES PRINT MOLINFO BIASVALUE TORSION REWEIGHT_BIAS READ RESTRAINT DUMPGRID
21.001 PLUMED syntax and analysis Bonomi M. Basic features of the PLUMED input syntax with a particular focus on PBCs and selection tools DUMPATOMS WHOLEMOLECULES ALPHARMSD ANTIBETARMSD PRINT PARABETARMSD MOLINFO GYRATION TORSION CENTER DISTANCE COMBINE
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 SORT CUSTOM LOCAL_Q1 MORE_THAN CLUSTER_PROPERTIES PAIRENTROPY CONCATENATE Q6 CLUSTER_WEIGHTS COM SPHERICAL_HARMONIC OUTER_PRODUCT FIXEDATOM MATRIX_PRODUCT SUM GATHER_REPLICAS CONSTANT RDF DISTANCES RESTRAINT TORSIONS DFSCLUSTERING DIAGONALIZE MEAN TORSION BIASVALUE REFERENCE_GRID A1_DENOM PRINT ONES DOMAIN_DECOMPOSITION CONTACT_MATIX GROUP VSTACK AVERAGE SPRINT COORDINATIONNUMBER DISTANCE INSPHERE KDE TRANSPOSE Q4 INTEGRATE_GRID MATRIX_VECTOR_PRODUCT DUMPGRID COMBINE GSYMFUNC_THREEBODY Q1 CONTACT_MATRIX MATHEVAL FIXED_ATOM HISTOGRAM ACCUMULATE LOCAL_AVERAGE LESS_THAN
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 UPPER_WALLS DUMPGRID OPES_METAD Q6 MATHEVAL HISTOGRAM LOWER_WALLS ENVIRONMENTSIMILARITY
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. DFSCLUSTERING FLUSH CLUSTER_NATOMS CMUMD PRINT GROUP COORDINATIONNUMBER CONTACT_MATRIX CLUSTER_DISTRIBUTION RESTRAINT
22.005 Machine learning collective variables with PyTorch Bonati L. An introduction to designing data-driven CVs using two methods (DeepLDA and DeepTICA). PRINT TORSION PYTORCH_MODEL
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 CLASSICAL_MDS UNITS PCAVARS FCCUBIC PATH MOLINFO RMSD COMMITTOR DUMPMULTICOLVAR PROJECT_ALL_ANALYSIS_DATA COLLECT_FRAMES TORSION PRINT COORDINATIONNUMBER PCA EUCLIDEAN_DISSIMILARITIES ANTIBETARMSD OUTPUT_ANALYSIS_DATA_TO_COLVAR MTRANSFORM_MORE DUMPGRID PARABETARMSD LANDMARK_SELECT_FPS OUTPUT_ANALYSIS_DATA_TO_PDB ALPHARMSD SKETCH_MAP HISTOGRAM
21.004 Metadynamics Bonomi M. How to calculate statistical averages and free energy surfaces using metadynamics REWEIGHT_BIAS TORSION DUMPGRID PRINT METAD MOLINFO CONVERT_TO_FES HISTOGRAM
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. UPPER_WALLS REWEIGHT_BIAS DUMPGRID CUSTOM PRINT METAD CONVERT_TO_FES READ AVERAGE CONSTANT HISTOGRAM COM UNITS DISTANCE COORDINATIONNUMBER RESTRAINT
20.001 Installing PLUMED Tribello G. An interactive tutorial resource on compiling PLUMED and linking it with MD codes.