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 July 10, 2024.
Suggestions for an order to work through the tutorials can be found here.
ID | Name | Instructors | Description | Actions | Modules |
---|---|---|---|---|---|
24.001 | hybrid Small Angle Scattering — hands-on guide | Ballabio F. | Practical guide to the use of the hySAS module. | SAXS MOLINFO GYRATION PRINT STATS ENSEMBLE BIASVALUE RESTRAINT | function bias colvar generic isdb |
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 | COORDINATIONNUMBER MORE_THAN DISTANCE_MATRIX CLUSTER_WEIGHTS MATRIX_PRODUCT CLUSTER_PROPERTIES Q4 POSITION INTERPOLATE_GRID MEAN OUTER_PRODUCT DOMAIN_DECOMPOSITION DISTANCE SELECT_COMPONENTS VOLUME CONCATENATE CENTER ACCUMULATE RDF KDE DFSCLUSTERING SORT Q1 COM HISTOGRAM LOWEST DIAGONALIZE GPATH INTEGRATE_GRID DISPLACEMENT INSPHERE CONTACT_MATRIX GSYMFUNC_THREEBODY FIXEDATOM CUSTOM PDB2CONSTANT LOCAL_Q1 GEOMETRIC_PATH GATHER_REPLICAS AVERAGE DISTANCES TORSION REFERENCE_GRID ONES PRINT LESS_THAN SUM TRANSPOSE SPRINT DIFFERENCE WHOLEMOLECULES Q6 RMSD_VECTOR RMSD PAIRENTROPY CONSTANT COMBINE SPHERICAL_HARMONIC EUCLIDEAN_DISTANCE PATH LOCAL_AVERAGE PCAVARS MATRIX_VECTOR_PRODUCT VSTACK DUMPGRID GROUP BIASVALUE RESTRAINT | adjmat multicolvar clusters function valtools vatom matrixtools gridtools bias mapping sprint colvar generic symfunc refdist core volumes |
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 | DISTANCE_MATRIX MORE_THAN HISTOGRAM ONES SUM MATRIX_VECTOR_PRODUCT MEAN DUMPGRID OPES_METAD GROUP MATHEVAL UPPER_WALLS CUSTOM LOWER_WALLS Q6 ENVIRONMENTSIMILARITY | adjmat envsim function matrixtools gridtools bias opes generic symfunc core |
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. | COORDINATIONNUMBER MORE_THAN FLUSH ONES PRINT CLUSTER_NATOMS MEAN MATRIX_VECTOR_PRODUCT SUM GROUP CONTACT_MATRIX RESTRAINT CLUSTER_DISTRIBUTION DFSCLUSTERING | adjmat clusters function matrixtools bias generic symfunc core |
22.005 | Machine learning collective variables with PyTorch | Bonati L. | An introduction to designing data-driven CVs using two methods (DeepLDA and DeepTICA). | PYTORCH_MODEL PRINT TORSION | pytorch colvar generic |
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 | COORDINATIONNUMBER MORE_THAN PROJECT_POINTS MOLINFO COLLECT_FRAMES SKETCHMAP HISTOGRAM COMMITTOR ALPHARMSD CLASSICAL_MDS TORSION DUMPMULTICOLVAR LANDMARK_SELECT_FPS PCA PRINT DUMPPDB DUMPVECTOR RMSD FCCUBIC PATH ANTIBETARMSD PCAVARS PARABETARMSD DUMPGRID GROUP UNITS | multicolvar function landmarks gridtools mapping dimred secondarystructure generic colvar symfunc core setup |
21.004 | Metadynamics | Bonomi M. | How to calculate statistical averages and free energy surfaces using metadynamics | CONVERT_TO_FES HISTOGRAM TORSION REWEIGHT_BIAS MOLINFO PRINT DUMPGRID METAD | bias gridtools generic 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. | CONVERT_TO_FES COM READ AVERAGE HISTOGRAM COORDINATIONNUMBER REWEIGHT_BIAS PRINT DUMPGRID DISTANCE METAD UPPER_WALLS CUSTOM RESTRAINT UNITS CONSTANT | vatom function gridtools bias colvar generic symfunc setup |
20.001 | Installing PLUMED | Tribello G. | An interactive tutorial resource on compiling PLUMED and linking it with MD codes. | ||
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. | MOLINFO SASA_HASEL SECONDARY_STRUCTURE_RMSD ALPHARMSD PARABETARMSD SUM GYRATION LOWEST LESS_THAN BIASVALUE ANTIBETARMSD PRINT | sasa generic function colvar secondarystructure bias |
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 | colvar generic |
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 | OPES_EXPANDED OPES_METAD_EXPLORE TORSION ECV_MULTITHERMAL ECV_UMBRELLAS_LINE OPES_METAD ENERGY | opes colvar |
21.007 | Optimizing PLUMED performances | Bonomi M. | Some lessons on monitoring and improving the performance of PLUMED and gromacs | DEBUG EFFECTIVE_ENERGY_DRIFT RMSD WHOLEMOLECULES COMBINE GROUP CUSTOM DISTANCE COORDINATION METAD PRINT | core generic function colvar bias |
21.005 | Replica exchange methods | Bussi G. | Runninge umbrella sampling with replica exchange, bias exchange metadynamics and parallel tempering metadynamics | MOLINFO RESTRAINT TORSION METAD RANDOM_EXCHANGES PRINT | colvar generic bias |
21.003 | Umbrella Sampling | Bussi G. | How to calculate statistical averages and free energy surfaces using umbrella sampling | CONVERT_TO_FES MOLINFO REWEIGHT_BIAS DUMPGRID RESTRAINT CUSTOM READ HISTOGRAM TORSION BIASVALUE PRINT | generic function gridtools colvar bias |
21.001 | PLUMED syntax and analysis | Bonomi M. | Basic features of the PLUMED input syntax with a particular focus on PBCs and selection tools | MOLINFO CENTER ALPHARMSD WHOLEMOLECULES GYRATION COMBINE DUMPATOMS ANTIBETARMSD TORSION DISTANCE PARABETARMSD PRINT | generic vatom function colvar secondarystructure |