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. | SASA_HASEL SUM PARABETARMSD GYRATION BIASVALUE ANTIBETARMSD MOLINFO PRINT SECONDARY_STRUCTURE_RMSD LOWEST ALPHARMSD LESS_THAN | generic sasa bias secondarystructure function colvar |
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 TORSION OPES_METAD_EXPLORE OPES_METAD ECV_UMBRELLAS_LINE ECV_MULTITHERMAL OPES_EXPANDED | colvar opes |
21.007 | Optimizing PLUMED performances | Bonomi M. | Some lessons on monitoring and improving the performance of PLUMED and gromacs | RMSD COORDINATION COMBINE DISTANCE WHOLEMOLECULES GROUP PRINT METAD DEBUG CUSTOM EFFECTIVE_ENERGY_DRIFT | generic core bias function colvar |
21.005 | Replica exchange methods | Bussi G. | Runninge umbrella sampling with replica exchange, bias exchange metadynamics and parallel tempering metadynamics | RESTRAINT TORSION RANDOM_EXCHANGES MOLINFO PRINT METAD | generic bias colvar |
21.003 | Umbrella Sampling | Bussi G. | How to calculate statistical averages and free energy surfaces using umbrella sampling | RESTRAINT TORSION DUMPGRID HISTOGRAM BIASVALUE CONVERT_TO_FES MOLINFO PRINT REWEIGHT_BIAS READ CUSTOM | generic gridtools bias function colvar |
21.001 | PLUMED syntax and analysis | Bonomi M. | Basic features of the PLUMED input syntax with a particular focus on PBCs and selection tools | COMBINE DISTANCE TORSION PARABETARMSD GYRATION WHOLEMOLECULES ANTIBETARMSD DUMPATOMS MOLINFO PRINT CENTER ALPHARMSD | generic vatom secondarystructure function colvar |
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 | COM DISTANCE VSTACK GSYMFUNC_THREEBODY DFSCLUSTERING LOCAL_Q1 CENTER PRINT GROUP INTERPOLATE_GRID RMSD PDB2CONSTANT VOLUME DIAGONALIZE SPRINT DISPLACEMENT CONSTANT TRANSPOSE BIASVALUE MATRIX_PRODUCT AVERAGE RDF WHOLEMOLECULES INSPHERE SELECT_COMPONENTS LOWEST Q1 DISTANCE_MATRIX FIXEDATOM INTEGRATE_GRID KDE ACCUMULATE ONES GPATH LOCAL_AVERAGE PAIRENTROPY DUMPGRID POSITION Q4 GEOMETRIC_PATH REFERENCE_GRID LESS_THAN SORT DOMAIN_DECOMPOSITION CUSTOM SUM COMBINE SPHERICAL_HARMONIC MEAN GATHER_REPLICAS CLUSTER_PROPERTIES PATH CLUSTER_WEIGHTS MORE_THAN CONTACT_MATRIX HISTOGRAM OUTER_PRODUCT Q6 CONCATENATE RMSD_VECTOR RESTRAINT DISTANCES TORSION PCAVARS MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER | adjmat volumes function matrixtools refdist vatom valtools sprint mapping generic bias symfunc core gridtools multicolvar clusters colvar |
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 | ENVIRONMENTSIMILARITY Q6 MATHEVAL OPES_METAD DISTANCE_MATRIX CUSTOM SUM ONES GROUP MEAN LOWER_WALLS HISTOGRAM MATRIX_VECTOR_PRODUCT DUMPGRID UPPER_WALLS MORE_THAN | adjmat function matrixtools generic bias symfunc core gridtools opes envsim |
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. | CLUSTER_NATOMS DFSCLUSTERING FLUSH SUM RESTRAINT ONES GROUP MEAN PRINT MORE_THAN CONTACT_MATRIX MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER CLUSTER_DISTRIBUTION | adjmat function matrixtools generic bias symfunc core clusters |
22.005 | Machine learning collective variables with PyTorch | Bonati L. | An introduction to designing data-driven CVs using two methods (DeepLDA and DeepTICA). | TORSION PYTORCH_MODEL PRINT | generic pytorch colvar |
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 MOLINFO UNITS ANTIBETARMSD PRINT RMSD COMMITTOR COLLECT_FRAMES LANDMARK_SELECT_FPS PCA DUMPGRID FCCUBIC PATH HISTOGRAM PARABETARMSD TORSION PCAVARS DUMPMULTICOLVAR ALPHARMSD COORDINATIONNUMBER | dimred mapping setup generic symfunc secondarystructure landmarks gridtools multicolvar colvar |
21.004 | Metadynamics | Bonomi M. | How to calculate statistical averages and free energy surfaces using metadynamics | CONVERT_TO_FES METAD MOLINFO REWEIGHT_BIAS TORSION PRINT HISTOGRAM DUMPGRID | bias generic gridtools colvar |
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. | READ AVERAGE CONVERT_TO_FES COM DISTANCE METAD CUSTOM RESTRAINT REWEIGHT_BIAS UNITS COORDINATIONNUMBER PRINT CONSTANT HISTOGRAM DUMPGRID UPPER_WALLS | function vatom generic bias setup symfunc gridtools colvar |
20.001 | Installing PLUMED | Tribello G. | An interactive tutorial resource on compiling PLUMED and linking it with MD codes. |