Browse the eggs in PLUMED-NEST
PLUMED-NEST provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation or analysis contained in a published paper. Furthermore, PLUMED-NEST monitors the compatibility of the provided PLUMED input files with the current and development versions of the code and integrates links from these files to the PLUMED manual.
Here is the list of projects already deposited in PLUMED-NEST, while a complete bibliography can be found here.
| plumID | Name | Category | Keywords | Contributor | Actions | Modules |
|---|---|---|---|---|---|---|
| 25.030 | Committor Regularization | methods | metadynamics, enhanced sampling, mlcvs, committor, machine learning | Florian Dietrich | UNITS METAD MOVINGRESTRAINT PRINT | setup generic bias |
| 25.029 | Energetic Constraints in the Enzymatic Depolymerization of Crystalline PET from enhanced molecular simulations | bio | HREX-Metadynamics, PETase, crystalline PET, amorphous PET, conformational ensembles, substrate binding, chain detachment | Ania Di Pede-Mattatelli and Francesco Colizzi | UPPER_WALLS DISTANCE MOLINFO LOWER_WALLS CONVERT_TO_FES REWEIGHT_BIAS PRINT DUMPGRID COM METAD WHOLEMOLECULES FIXEDATOM HISTOGRAM | gridtools colvar vatom generic bias |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | PYTORCH_MODEL DISTANCE UPPER_WALLS UNITS BIASVALUE POSITION ENDPLUMED LOWER_WALLS PRINT RMSD GROUP OPES_METAD CUSTOM METAD ENERGY WHOLEMOLECULES MOLINFO TORSION | colvar function generic core opes pytorch setup bias |
| 25.007 | Shaping the glycan landscape. Hidden relationships between linkage and ring distortion induced by carbohydrate-active enzmyes | bio | REST-RECT, REST2, glycan, enzyme, CAZyme, steered | Isabell Grothaus | PUCKERING RESTRAINT DISTANCE MOVINGRESTRAINT PRINT METAD RESTART MOLINFO TORSION | setup colvar generic bias |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | DISTANCE COORDINATION COMBINE PRINT GROUP OPES_METAD CUSTOM ENERGY LOAD TORSION | colvar function core generic opes setup |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | RMSD COM ECV_MULTITHERMAL CUSTOM CONSTANT TORSION RESTART PROJECTION_ON_AXIS INCLUDE METAD OPES_METAD_EXPLORE WHOLEMOLECULES MOLINFO UPPER_WALLS WRAPAROUND LOWER_WALLS OPES_EXPANDED MATHEVAL COORDINATION GROUP PRINT ENERGY CONTACTMAP BIASVALUE | colvar vatom function generic core opes setup bias |
| 24.013 | Estimating Free Energy Surfaces and their Convergence from multiple, independent static and history-dependent biased molecular-dynamics simulations with Mean Force Integration | methods | Mean Force Integration, Convergence, FES, Umbrella Sampling | Matteo Salvalaglio | COMMITTOR RESTRAINT DISTANCE FLUSH MOLINFO COORDINATIONNUMBER MATHEVAL PRINT METAD ENERGY RESTART BIASVALUE TORSION | colvar function generic setup symfunc bias |
| 24.000 | Ammonia Decomposition on Non-stoichiometric Lithium Imide | chemistry | ammonia decomposition, non-stoichiometric lithium imide, machine learning interatomic potentials, enhanced sampling, heterogeneous catalysis | Francesco Mambretti | UPPER_WALLS DISTANCE UNITS FLUSH COORDINATIONNUMBER GROUP ZDISTANCES PRINT OPES_METAD FIXEDATOM | colvar vatom generic core multicolvar opes setup symfunc bias |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | UPPER_WALLS DRR FLUSH LOWER_WALLS PRINT CUSTOM METAD PATHMSD BIASVALUE | colvar function generic bias drr |
| 23.004 | Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point | chemistry | water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential | Pablo Piaggi | UPPER_WALLS LOWER_WALLS OPES_EXPANDED ECV_UMBRELLAS_LINE PRINT DUMPGRID ENVIRONMENTSIMILARITY RESTART HISTOGRAM | gridtools envsim generic opes setup bias |
| 23.000 | Atomistic simulations of RNA tetraloop folding via PTWTE-WTM | bio | parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding | Gül Zerze | UPPER_WALLS LOWER_WALLS PRINT METAD ENERGY CONTACTMAP WHOLEMOLECULES | colvar generic bias |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | Q6 COORDINATIONNUMBER PAIRENTROPY CENTER GROUP COMBINE MATHEVAL PRINT INCLUDE Q4 METAD LOAD | gridtools vatom function core generic setup symfunc bias |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | DISTANCE DISTANCES METAD PRINT | colvar multicolvar generic bias |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | UPPER_WALLS FLUSH MOLINFO GHBFIX COORDINATION COMBINE GROUP PRINT CUSTOM METAD LOAD BIASVALUE | colvar function core generic setup bias |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | COMMITTOR PYTORCH_MODEL DISTANCE POSITION RMSD CUSTOM CONSTANT TORSION ENDPLUMED INCLUDE WHOLEMOLECULES MOLINFO COMBINE OPES_METAD UNITS PRINT GROUP ENERGY CONTACTMAP BIASVALUE | colvar function generic core opes pytorch setup bias |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | TORSION WHOLEMOLECULES PRINT | colvar generic |
| 22.012 | Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT | bio | contact maps, protein-protein interactions | Isabell-Louise Grothaus | CONTACTMAP DISTANCE CENTER PRINT | vatom colvar generic |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | RESTRAINT UPPER_WALLS UNITS LOWER_WALLS COMBINE MOVINGRESTRAINT PRINT ENSEMBLE CUSTOM METAD CONSTANT LOAD TORSION | colvar function generic setup bias |
| 21.041 | Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics | methods | metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions | Matej Badin | ENDPLUMED COORDINATION COMBINE PRINT VOLUME CUSTOM METAD | colvar generic function bias |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | COORDINATIONNUMBER COMBINE CENTER PRINT GROUP INCLUDE VOLUME METAD ENERGY LOAD | colvar vatom function generic core setup symfunc bias |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | UPPER_WALLS DISTANCE ALPHARMSD LOWER_WALLS PRINT MATHEVAL INCLUDE METAD ENERGY CONTACTMAP WHOLEMOLECULES MOLINFO | colvar secondarystructure function generic bias |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | DISTANCE UNITS PRINT REWEIGHT_METAD INCLUDE CUSTOM METAD CONSTANT ENERGY BIASVALUE TORSION | colvar function generic setup bias |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | RESTRAINT DISTANCE MOLINFO SAXS CENTER GROUP PRINT STATS INCLUDE ENSEMBLE WHOLEMOLECULES BIASVALUE | colvar vatom isdb generic core function bias |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | PYTORCH_MODEL DISTANCE UPPER_WALLS ENDPLUMED COORDINATION CENTER GROUP MATHEVAL ANGLE OPES_METAD PRINT ENERGY WHOLEMOLECULES FIXEDATOM FIT_TO_TEMPLATE | colvar vatom function generic core opes pytorch bias |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | UPPER_WALLS DISTANCE GYRATION PRINT COM METAD ENERGY MOLINFO | vatom colvar generic bias |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | UPPER_WALLS DISTANCE LOWER_WALLS CENTER GROUP PRINT COM METAD RESTART | colvar vatom core generic setup bias |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | UPPER_WALLS UNITS CELL LOWER_WALLS ENDPLUMED PRINT METAD AROUND FCCUBIC | colvar generic setup volumes symfunc bias |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | CLUSTER_DISTRIBUTION LOCAL_Q6 CLUSTER_NATOMS Q6 DISTANCES SMAC CLUSTER_PROPERTIES COORDINATIONNUMBER PRINT MATRIX_VECTOR_PRODUCT ONES OUTPUT_CLUSTER CUSTOM DFSCLUSTERING MORE_THAN CONTACT_MATRIX OUTER_PRODUCT METAD | clusters function generic multicolvar matrixtools adjmat symfunc bias |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | COORDINATION GROUP EXTERNAL METAD ENERGY | colvar core bias |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | RESTRAINT DISTANCE EDS COMBINE PRINT TORSION | colvar eds function generic bias |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | UPPER_WALLS CELL ENDPLUMED LOWER_WALLS COMBINE PRINT MATHEVAL VOLUME METAD ENERGY TORSION | colvar generic function bias |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | ENDPLUMED ERMSD PRINT RMSD METAD WHOLEMOLECULES MOLINFO | colvar generic bias |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | EMMI PRINT GROUP BIASVALUE WHOLEMOLECULES MOLINFO | core isdb generic bias |
| 26.005 | Cryptic pocket discovery in Alzheimer disease risk proteins BIN1, PICALM, and CD2AP via well-tempered metadynamics | methods | cryptic pockets, Alzheimer disease, BIN1, PICALM, CD2AP, well-tempered metadynamics, endocytosis, clathrin-mediated trafficking, virtual screening | Cagrı Ozkurt | DISTANCE ANGLE METAD WHOLEMOLECULES PRINT | colvar bias generic |
| 25.026 | Deciphering the Molecular Mechanisms of Startle Disease - the Role of the Asn46Lys Mutation in the Glycine Receptor | bio | metadynamics, glycine receptors, funnel metadynamics | Jacob Adam Clark | FUNNEL_PS FUNNEL METAD LOWER_WALLS PRINT COM UPPER_WALLS | vatom bias funnel generic |
| 25.005 | Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations | chemistry | WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD | Vikas Tiwari, Tarak Karmakar | COM DISTANCE ANGLE FIXEDATOM METAD DISTANCES LOWER_WALLS PRINT UNITS FLUSH COORDINATION COORDINATIONNUMBER COMBINE UPPER_WALLS GROUP RESTRAINT | vatom setup multicolvar bias symfunc function colvar core generic |
| 24.018 | A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations | chemistry | prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning | Léon HUET | PRINT DISTANCE | colvar generic |
| 23.030 | Data Driven Classification of Ligand Unbinding Pathways | bio | OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time | Dhiman Ray | FIT_TO_TEMPLATE POSITION WRAPAROUND WHOLEMOLECULES FLUSH CUSTOM ENERGY DISTANCE LOWER_WALLS TORSION OPES_METAD_EXPLORE UPPER_WALLS BIASVALUE MOLINFO COMMITTOR ENDPLUMED UNITS MATHEVAL CENTER PRINT COORDINATION COM GROUP OPES_METAD | setup vatom bias function colvar core generic opes |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | PCAVARS METAD LOWER_WALLS WHOLEMOLECULES PRINT UPPER_WALLS | mapping bias generic |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | DISTANCE MOLINFO PRINT COM UPPER_WALLS PBMETAD GYRATION | colvar vatom bias generic |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | BF_FOURIER VES_LINEAR_EXPANSION TD_UNIFORM OPT_AVERAGED_SGD TORSION PRINT | colvar ves generic |
| 20.002 | Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study | bio | Metadynamics, path CVs | Riccardo Ocello | RESTART METAD PATHMSD MOLINFO WHOLEMOLECULES PRINT UPPER_WALLS GROUP | setup bias colvar core generic |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | INCLUDE SORT DISTANCE MAXENT MOLINFO METAD TORSION WHOLEMOLECULES PRINT COORDINATION FLUSH COM MATHEVAL | vatom bias function colvar generic |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | RESTART INPLANEDISTANCES DISTANCES PRINT FLUSH COM MOVINGRESTRAINT | vatom setup multicolvar bias generic |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | RMSD FUNNEL_PS DISTANCE FUNNEL METAD LOWER_WALLS WHOLEMOLECULES PRINT COM UPPER_WALLS | vatom bias colvar funnel generic |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | RESTART ANTIBETARMSD MOLINFO LOWER_WALLS WHOLEMOLECULES PRINT ENDPLUMED ALPHABETA CS2BACKBONE FLUSH UPPER_WALLS PBMETAD GROUP BIASVALUE | setup multicolvar secondarystructure isdb bias core generic |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | RESTART EXTERNAL DISTANCE COMMITTOR WHOLEMOLECULES PRINT TORSION ALPHABETA COM COMBINE | setup vatom multicolvar bias function colvar generic |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | MOLINFO COMMITTOR METAD PRINT ALPHABETA FLUSH COMBINE | function multicolvar bias generic |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | COMBINE MOLINFO METAD ERMSD WHOLEMOLECULES | colvar bias generic function |
| 24.035 | Data efficient machine learning potentials for modeling catalytic reactivity via active learning and enhanced sampling | chemistry | opes, catalysis, ammonia, machine learning potentials | Luigi Bonati | RESTART LOWER_WALLS OPES_METAD CUSTOM PRINT GROUP COMMITTOR COORDINATION UPPER_WALLS DISTANCE UNITS | generic core opes colvar bias setup function |
| 24.023 | Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21. A Machine-Learning-Aided Enhanced Sampling Study | bio | RNA, miRNA, OneOPES, ligand binding, conformational changes | Valerio Rizzi | RESTART COMBINE CUSTOM PRINT GROUP ENERGY TORSION ECV_MULTITHERMAL COORDINATION OPES_EXPANDED DISTANCE OPES_METAD_EXPLORE | generic core opes colvar setup function |
| 24.021 | Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state | chemistry | ion pairing, caco3, opes, proton transfer, crystallization | Pablo Piaggi | OPES_METAD PRINT ENERGY COORDINATION UPPER_WALLS DISTANCE | colvar bias generic opes |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | MOLINFO PRINT GROUP RESTRAINT EMMIVOX BIASVALUE INCLUDE ERMSD WHOLEMOLECULES | generic isdb core colvar bias |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | RESTART PRINT METAD TORSION UNITS | colvar bias setup generic |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | COMBINE PRINT METAD DISTANCE WHOLEMOLECULES UNITS | generic colvar bias setup function |
| 23.041 | Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference | methods | EMMIVox, cryo-EM, single-structure refinement, ensemble refinement, Bayesian inference, B-factors, structural ensembles | Samuel Hoff | MOLINFO PRINT GROUP EMMIVOX WRAPAROUND BIASVALUE INCLUDE UPPER_WALLS DISTANCE WHOLEMOLECULES | generic isdb core colvar bias |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | MOLINFO LOWER_WALLS PRINT GYRATION COM UPPER_WALLS DISTANCE PBMETAD | colvar bias vatom generic |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | COMBINE FIT_TO_TEMPLATE MOLINFO ANN ALPHARMSD PRINT METAD WHOLEMOLECULES POSITION | generic secondarystructure colvar bias annfunc function |
| 23.029 | An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations | bio | SAXS, SANS, SAS, metainference, proteins, nucleic-acid | Federico Ballabio | MOLINFO RMSD PRINT STATS ENSEMBLE GROUP CENTER WRAPAROUND SAXS UPPER_WALLS DISTANCE BIASVALUE | generic isdb core colvar bias vatom function |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | DISTANCES LOWER_WALLS FLUSH OPES_METAD ZDISTANCES COORDINATIONNUMBER PRINT GROUP CUSTOM ENERGY FIXEDATOM COMMITTOR COM UPPER_WALLS DISTANCE MATHEVAL UNITS | multicolvar generic symfunc core opes colvar bias vatom setup function |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | COMBINE LOWER_WALLS COORDINATIONNUMBER PRINT GROUP METAD LOCAL_Q6 MOVINGRESTRAINT MFILTER_MORE Q6 | multicolvar generic symfunc core bias function |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | PRINT GYRATION COM COORDINATION UPPER_WALLS DISTANCE PBMETAD | colvar bias vatom generic |
| 23.016 | Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action | bio | G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics | Timothy Clark | MOLINFO RMSD REWEIGHT_METAD PRINT METAD DUMPGRID READ MATHEVAL WHOLEMOLECULES DISTANCE CONVERT_TO_FES HISTOGRAM | generic gridtools colvar bias function |
| 23.010 | An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands | bio | GPCR, binding free energy, free energy surface | Timothy Clark | LOWER_WALLS CONSTANT PRINT METAD WHOLEMOLECULES UPPER_WALLS DISTANCE BIASVALUE MATHEVAL | colvar bias generic function |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | MOLINFO PRINT GROUP TORSION GYRATION PBMETAD WHOLEMOLECULES | colvar bias core generic |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | MOLINFO ALPHARMSD PRINT METAD CONTACTMAP COM DISTANCE ANGLE DUMPFORCES | generic secondarystructure colvar bias vatom |
| 22.021 | Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn Løland Bore | LOWER_WALLS PRINT INCLUDE ENVIRONMENTSIMILARITY OPES_EXPANDED UPPER_WALLS ECV_UMBRELLAS_LINE | bias envsim generic opes |
| 21.046 | Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs | bio | wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder | Elena Papaleo | LOWER_WALLS ALPHABETA METAD GROUP PRINT ENDPLUMED GYRATION UPPER_WALLS WHOLEMOLECULES | multicolvar generic core colvar bias |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | RESTART MOLINFO FLUSH PRINT ENERGY TORSION EXTERNAL | colvar bias setup generic |
| 21.010 | Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry | chemistry | Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis | Théo Magrino | generic | |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | OPES_METAD PRINT ENERGY TORSION ENDPLUMED ECV_MULTITHERMAL OPES_EXPANDED ECV_UMBRELLAS_LINE | colvar generic opes |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | MOLINFO ALPHARMSD FLUSH PRINT GROUP CENTER GYRATION BIASVALUE SAXS PBMETAD WHOLEMOLECULES EEFSOLV METAINFERENCE | generic secondarystructure isdb core colvar bias vatom |
| 20.034 | Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations | bio | RNA, SARS-CoV-2, partial tempering | Sandro Bottaro | RESTART MOLINFO PRINT TORSION CENTER ABMD ERMSD DISTANCE | generic colvar bias vatom setup |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | PRINT TORSION ENDPLUMED | colvar generic |
| 20.021 | Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. | bio | phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution | Cristina Paissoni | MOLINFO PRINT STATS RESTRAINT COORDINATION WHOLEMOLECULES | colvar bias generic function |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | MOLINFO DIHCOR ALPHABETA PRINT GYRATION INCLUDE COORDINATION PBMETAD WHOLEMOLECULES | colvar bias multicolvar generic |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | RESTART COMBINE DISTANCES FLUSH COORDINATIONNUMBER METAD GROUP PRINT ENDPLUMED UPPER_WALLS UNITS | multicolvar generic symfunc core bias setup function |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | COMBINE CUSTOM PRINT GROUP TORSION RESTRAINT CENTER ENDPLUMED DISTANCE ANGLE DUMPDERIVATIVES | generic core colvar bias vatom function |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | MOLINFO RMSD PRINT METAD TORSION ERMSD DISTANCE WHOLEMOLECULES | colvar bias generic |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | OPES_METAD PRINT METAD TORSION ENDPLUMED EXTERNAL POSITION UNITS | generic opes colvar bias setup |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | COMBINE RESTRAINT COM ANN POSITION | colvar bias vatom annfunc function |
| 19.046 | Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding | bio | VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation | Faidon Brotzakis | COMBINE FUNNEL LOWER_WALLS MOLINFO RMSD DISTANCES REWEIGHT_METAD ALPHABETA METAD GROUP PRINT TORSION COM UPPER_WALLS DISTANCE WHOLEMOLECULES BRIDGE | multicolvar generic funnel adjmat core colvar bias vatom function |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | RESTART PATH DISTANCES FLUSH PRINT METAD UPPER_WALLS | multicolvar generic mapping bias setup |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | MOLINFO FLUSH RDC PRINT STATS ENSEMBLE TORSION ENDPLUMED GYRATION JCOUPLING WHOLEMOLECULES CS2BACKBONE PBMETAD BIASVALUE METAINFERENCE | generic isdb colvar bias function |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | PRINT METAD TORSION GYRATION WHOLEMOLECULES | colvar bias generic |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | CONSTANT PRINT METAD TORSION BIASVALUE MATHEVAL WHOLEMOLECULES | colvar bias generic function |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | MOLINFO DIHCOR DHENERGY RDC ALPHABETA PRINT GROUP ENSEMBLE STATS TORSION ENDPLUMED CENTER RESTRAINT UPPER_WALLS DISTANCE WHOLEMOLECULES PBMETAD METAINFERENCE | multicolvar generic isdb core colvar bias vatom function |
| 25.012 | A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis | bio | enzyme catalysis, transition state, structure-activity relationship, free energy surface, reaction mechanism, water, alpha-amylase, sugar, QM/MM MD, OPES, committor function, machine learning | Sudip Das | CELL INCLUDE BIASVALUE UNITS CUSTOM ENERGY DISTANCE TORSION POSITION FLUSH MATHEVAL COORDINATION LOAD COMBINE PRINT OPES_METAD | setup bias opes function colvar generic |
| 25.004 | Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride | chemistry | OPES, OPES flooding, Catalysis, Ammonia Synthesis | Axel Tosello Gardini | DISTANCES UNITS CUSTOM DISTANCE FLUSH UPPER_WALLS COMMITTOR ZDISTANCES COORDINATIONNUMBER GROUP PRINT FIXEDATOM OPES_METAD | setup bias vatom symfunc opes function multicolvar core colvar generic |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | FUNCPATHGENERAL DISTANCE METAD COM WHOLEMOLECULES RESTART MOLINFO GROUP PRINT UPPER_WALLS | setup bias vatom function core colvar generic |
| 24.036 | Leveraging cryptic ligand envelopes through enhanced molecular simulations | bio | HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope | Francesco Colizzi | DUMPGRID TORSION DISTANCE WHOLEMOLECULES HISTOGRAM COORDINATION GROUP PRINT ANGLE CONVERT_TO_FES | core gridtools colvar generic |
| 24.033 | Transient interactions between the fuzzy coat and the cross-b core of brain-derived Ab42 filaments | bio | CryoEM, MEMMI, Metadynamics, Metainference, Ab42 Fibrils, structural ensemble | Maria Milanesi | DUMPMASSCHARGE ALPHARMSD BIASVALUE PARABETARMSD EMMI PBMETAD DISTANCE DUMPATOMS COM WHOLEMOLECULES RMSD COORDINATION MOLINFO CENTER GROUP PRINT UPPER_WALLS | bias vatom secondarystructure core isdb colvar generic |
| 24.024 | Host-Guest binding free energies à la carte, an automated OneOPES protocol | bio | OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest | Valerio Rizzi | FIXEDATOM OPES_EXPANDED ENDPLUMED FIT_TO_TEMPLATE ECV_MULTITHERMAL OPES_METAD_EXPLORE DISTANCE TORSION ENERGY GROUP WHOLEMOLECULES MATHEVAL COORDINATION CENTER ANGLE LOWER_WALLS PRINT UPPER_WALLS | vatom opes bias function core colvar generic |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | TORSION METAD FLUSH WHOLEMOLECULES RESTART PRINT | bias setup colvar generic |
| 23.045 | Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state | bio | Path CVs Metadynamics, GPCRs activation transition | Vittorio Limongelli | INCLUDE ALPHARMSD CONTACTMAP DISTANCE METAD PATHMSD FUNCPATHMSD MOLINFO LOWER_WALLS PRINT UPPER_WALLS | bias secondarystructure function colvar generic |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | BIASVALUE ENDPLUMED UNITS POSITION CUSTOM PYTORCH_MODEL LOWER_WALLS PRINT UPPER_WALLS OPES_METAD | pytorch setup bias opes function colvar generic |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | OPES_EXPANDED CONTACTMAP ECV_MULTITHERMAL ECV_UMBRELLAS_LINE WHOLEMOLECULES ENERGY PRINT | opes colvar generic |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | OPES_EXPANDED ENDPLUMED UNITS ECV_MULTITHERMAL POSITION TORSION ENERGY PRINT OPES_METAD | opes colvar setup generic |
| 22.034 | Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods | materials | metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene | Matteo Salvalaglio | CELL DRMSD CUSTOM METAD MATHEVAL COMMITTOR LOWER_WALLS PRINT UPPER_WALLS | bias function colvar generic |
| 21.036 | Modelling the structure and interactions of intrinsically disordered peptides with multiple-replica, metadynamics-based sampling methods and force-field combinations | bio | Bias Exchange Metadynamics, PTWTE-metaD | Matteo Salvalaglio | ALPHARMSD RANDOM_EXCHANGES ANTIBETARMSD PARABETARMSD ENERGY METAD GROUP WHOLEMOLECULES GYRATION COORDINATION MOLINFO DIHCOR LOWER_WALLS PRINT UPPER_WALLS | bias secondarystructure multicolvar core colvar generic |
| 21.030 | Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains | bio | parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure | Jim Pfaendtner | ALPHABETA INCLUDE PBMETAD DISTANCE TORSION METAD COM GYRATION COORDINATION ENERGY PRINT | bias vatom multicolvar colvar generic |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | UNITS DISTANCE METAD PATHMSD COM WHOLEMOLECULES PRINT UPPER_WALLS | setup bias vatom colvar generic |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | INCLUDE ERMSD CUSTOM METAD GROUP WHOLEMOLECULES GYRATION SAXS MOLINFO LOWER_WALLS PRINT UPPER_WALLS | bias function core isdb colvar generic |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | DISTANCES VES_LINEAR_EXPANSION DISTANCE EXTERNAL RESTRAINT COORDINATIONNUMBER COMBINE DUMPGRID OPT_AVERAGED_SGD METAD FLUSH LOAD UWALLS LOWER_WALLS ANGLES UNITS BF_CHEBYSHEV HISTOGRAM COORDINATION UPPER_WALLS CONVERT_TO_FES REWEIGHT_METAD REWEIGHT_BIAS TD_GRID PRINT | setup bias symfunc function gridtools multicolvar ves colvar generic |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | FUNNEL DISTANCE METAD COM FUNNEL_PS LOWER_WALLS PRINT UPPER_WALLS | bias vatom funnel colvar generic |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | DISTANCE COM WHOLEMOLECULES GROUP PRINT | vatom colvar generic core |
| 20.012 | Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies | bio | metadynamics, well-tempered ensemble, ligand binding, binding affinity calculations, novel COLVAR, funnel restraints, Hamiltonian replica-exchange, PathCV, COMetPath, SWISH | Francesco Gervasio | INCLUDE FUNCPATHGENERAL CONTACTMAP BIASVALUE PROJECTION_ON_AXIS DISTANCE METAD LOWER_WALLS COM GROUP WHOLEMOLECULES MATHEVAL LOAD MOLINFO CONSTANT PRINT UPPER_WALLS | setup bias vatom function core colvar generic |
| 20.005 | Muscarinic M2 receptor/ligand Frequency-Adaptive Metadynamics and QM/MM calculations | bio | Frequency-adaptive metadynamics, multiple-walkers metadynamics, well-tempered metadynamics, GPCR, receptor, Adiabatic Bias MD | Riccardo Capelli | ABMD ENDPLUMED DISTANCE FUNCPATHMSD WHOLEMOLECULES COMBINE DUMPGRID METAD COM FLUSH MOLINFO LOWER_WALLS HISTOGRAM UPPER_WALLS CONVERT_TO_FES CONTACTMAP REWEIGHT_METAD READ PRINT | bias vatom function gridtools colvar generic |
| 20.000 | Muscarinic M2 receptor-ligand funnel metadynamics | bio | multiple walker metadynamics, well-tempered metadynamics, funnel metadynamics, MC-HLDA, GPCR, receptor, Adiabatic Bias MD | Riccardo Capelli | DUMPGRID ABMD ENDPLUMED REWEIGHT_METAD READ DISTANCE METAD LOWER_WALLS COM MATHEVAL HISTOGRAM COMBINE PRINT UPPER_WALLS CONVERT_TO_FES | bias vatom function gridtools colvar generic |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | DUMPGRID OPT_AVERAGED_SGD UNITS VES_LINEAR_EXPANSION DISTANCE LOWER_WALLS TD_GRID BF_CHEBYSHEV FLUSH EXTERNAL COORDINATION UPPER_WALLS HISTOGRAM COMBINE PRINT ANGLE TD_WELLTEMPERED CONVERT_TO_FES | setup bias function gridtools ves colvar generic |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | MOVINGRESTRAINT ENDPLUMED UNITS GYRATION PRINT | bias colvar setup generic |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | INCLUDE RANDOM_EXCHANGES TORSION METAD PRINT | bias colvar generic |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | CONSTANT BIASVALUE DISTANCE METAD COM WHOLEMOLECULES MATHEVAL LOWER_WALLS PRINT UPPER_WALLS | bias vatom function colvar generic |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | DISTANCES UNITS DISTANCE METAD FLUSH RESTART COMBINE PRINT UPPER_WALLS | setup bias function multicolvar colvar generic |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | ENDPLUMED TORSION METAD MATHEVAL PRINT | bias function colvar generic |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | UNITS DISTANCE METAD FLUSH MATHEVAL RESTART PRINT UPPER_WALLS | setup bias function colvar generic |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | DISTANCE TORSION COM RESTRAINT GROUP PRINT | vatom bias core colvar generic |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | ALPHABETA METAD GROUP GYRATION WHOLEMOLECULES MOLINFO LOWER_WALLS PRINT UPPER_WALLS | bias multicolvar core colvar generic |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | CLUSTER_WITHSURFACE CONTACT_MATRIX MFILTER_MORE ENDPLUMED Q6 CLUSTER_NATOMS FLUSH DFSCLUSTERING COMMITTOR OUTPUT_CLUSTER LOCAL_Q6 | adjmat symfunc clusters multicolvar generic |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | ENDPLUMED DISTANCES METAD GYRATION RESTART COORDINATIONNUMBER PRINT | setup bias symfunc multicolvar colvar generic |
| 26.002 | A Transferable and Robust Computational Framework for Class A GPCR Activation Free Energies | bio | OneOPES, GPCR, ADRB1, activation, euclidean path, microswitches, conformational changes, allostery | Valerio Rizzi | ENERGY PATHMSD PATH PRINT UPPER_WALLS CUSTOM ECV_MULTITHERMAL CENTER VOLUME GROUP OPES_METAD_EXPLORE COORDINATION DISTANCE LOWER_WALLS OPES_EXPANDED RMSD | generic mapping function core opes bias vatom colvar |
| 25.028 | Designing transferable transition state guided collective variable via interpretable machine learning model for enhanced sampling. A case study on polymer collapse transition | bio | metadynamics, polymer collapse transition, transferable CV,interpretable ML-model | Saikat Dhibar and Biman Jana | PRINT UPPER_WALLS CENTER COMBINE GROUP COORDINATION DISTANCE LOWER_WALLS GYRATION WHOLEMOLECULES MATHEVAL METAD | generic function core bias vatom colvar |
| 25.024 | Sampling glycan-glycan interactions for B22 calculations | bio | B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange | Isabell Louise Grothaus | PRINT POSITION RESTRAINT COMBINE DISTANCE COM METAD | generic function bias vatom colvar |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | MOLINFO TORSION PRINT UPPER_WALLS SAXS ENSEMBLE CENTER METAINFERENCE FLUSH PBMETAD DISTANCE STATS GYRATION WHOLEMOLECULES | generic isdb function bias vatom colvar |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | RESTART PRINT UPPER_WALLS PBMETAD DISTANCE LOWER_WALLS UNITS MULTI_RMSD MATHEVAL | generic setup function bias colvar |
| 24.025 | Correlating Enzymatic Reactivity for Different Substrates using Transferable Data-Driven Collective Variables | bio | enzymatic reactivity, k_cat, transfer learning, data-driven CVs, catalysis, ligand-binding modes, water, alpha-amylase, sugar, classical MD, OPES, machine learning, Deep TDA CV, path CV | Sudip Das | RESTART TORSION PRINT PATH PYTORCH_MODEL UPPER_WALLS CUSTOM FIT_TO_TEMPLATE CENTER GROUP COORDINATION DISTANCE LOWER_WALLS OPES_METAD FIXEDATOM WHOLEMOLECULES | function generic setup pytorch mapping colvar core opes bias vatom |
| 24.019 | Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning | bio | OPES, machine learning, protein folding, adaptive sampling | Mingyuan Zhang | MOLINFO ALPHARMSD TORSION PRINT CUSTOM COMBINE COORDINATION DISTANCE OPES_METAD GYRATION WHOLEMOLECULES | function secondarystructure generic colvar opes |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | MOLINFO BIASVALUE PRINT UPPER_WALLS CENTER COMBINE GHBFIX GROUP COORDINATION DISTANCE LOWER_WALLS DEBUG COM METAD | function generic colvar core bias vatom |
| 23.043 | Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling | materials | Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters | Lorenzo Gigli | SELECT_COMPONENTS TRANSPOSE INCLUDE PRINT FLUSH SUM MATHEVAL METAD | generic matrixtools function bias valtools |
| 23.033 | DNA G-quadruplex and G-hairpin folding with ST-metaD protocol | bio | DNA, G4, GQ, quadruplex, hairpin, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | ERMSD MOLINFO BIASVALUE PRINT COMBINE GHBFIX COORDINATION WHOLEMOLECULES METAD | generic function bias colvar |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | RESTART DISTANCES POSITION PRINT UPPER_WALLS FLUSH FIT_TO_TEMPLATE GROUP DISTANCE LOWER_WALLS UNITS WRAPAROUND MATHEVAL WHOLEMOLECULES COM DUMPATOMS METAD | function generic setup multicolvar colvar core bias vatom |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | PRINT TORSION UPPER_WALLS CUSTOM CENTER DISTANCE FIXEDATOM MATHEVAL METAD | generic function bias vatom colvar |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | TORSION PRINT UPPER_WALLS FLUSH COMBINE DISTANCE WHOLEMOLECULES COM METAD | generic function bias vatom colvar |
| 23.009 | Deep Learning Collective Variables from Transition Path Ensemble | methods | TPI-Deep-TDA, Deep-TDA, Transition Path, OPES, OPES Flooding, Machine Learning, Protein folding, Ligand binding | Dhiman Ray | PRINT ENERGY PYTORCH_MODEL UPPER_WALLS GROUP COMBINE COORDINATION ENDPLUMED CUSTOM CENTER LOWER_WALLS ANGLE WHOLEMOLECULES RMSD MOLINFO INCLUDE FIT_TO_TEMPLATE CONTACTMAP DISTANCE COMMITTOR OPES_METAD FIXEDATOM MATHEVAL | function generic pytorch colvar core opes bias vatom |
| 22.016 | Homogeneous ice nucleation in an ab initio machine learning model of water | chemistry | ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces | Pablo Piaggi | RESTART PRINT ENERGY VOLUME UPPER_WALLS CUSTOM DUMPGRID OPES_METAD HISTOGRAM AROUND ENVIRONMENTSIMILARITY | gridtools volumes generic setup envsim function opes bias colvar |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | MOLINFO PRINT COORDINATIONNUMBER COMBINE DISTANCE COM COMMITTOR WHOLEMOLECULES RMSD METAD | function generic colvar symfunc bias vatom |
| 22.008 | Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters | materials | Well tempered metadynamics, ab-initio, ase | Daniel Sucerquia | UPPER_WALLS FLUSH COORDINATIONNUMBER COMBINE COORDINATION LOWER_WALLS DISTANCE UNITS GYRATION COM METAD | function generic setup colvar symfunc bias vatom |
| 22.005 | Collective Variable for Metadynamics Derived from AlphaFold Output | bio | AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable | Vojtech Spiwok | LOAD WHOLEMOLECULES PRINT METAD | generic setup bias |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | PRINT PYTORCH_MODEL UPPER_WALLS CUSTOM LOAD GROUP OPES_METAD_EXPLORE COORDINATION DISTANCE LOWER_WALLS UNITS OPES_METAD COM MATHEVAL | generic setup pytorch function core opes bias vatom colvar |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | MOLINFO INCLUDE PRINT CENTER CONTACTMAP COORDINATION DISTANCE ANTIBETARMSD UNITS ALPHARMSD RANDOM_EXCHANGES METAD | secondarystructure generic setup colvar bias vatom |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | MOLINFO ENERGY PRINT UPPER_WALLS PBMETAD LOWER_WALLS DISTANCE GYRATION COM | generic bias vatom colvar |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | BIASVALUE PRINT UPPER_WALLS REWEIGHT_METAD COMBINE DUMPGRID CUSTOM FLUSH VES_LINEAR_EXPANSION METAD MOVINGRESTRAINT REWEIGHT_BIAS LOAD CONVERT_TO_FES UNITS BF_CHEBYSHEV HISTOGRAM ANN RESTRAINT OPT_AVERAGED_SGD COORDINATIONNUMBER TD_WELLTEMPERED DISTANCE OPES_METAD CONSTANT | gridtools ves generic setup opes function annfunc symfunc bias colvar |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | RESTART MOLINFO PRINT REWEIGHT_BIAS ALPHABETA GROUP CONTACTMAP PBMETAD ALPHARMSD WHOLEMOLECULES METAD | secondarystructure generic setup multicolvar colvar core bias |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | PRINT RESTRAINT AROUND MFILTER_MORE COORDINATIONNUMBER LOAD GROUP DUMPGRID DFSCLUSTERING DENSITY FIXEDATOM CLUSTER_DISTRIBUTION CONTACT_MATRIX CLUSTER_NATOMS MULTICOLVARDENS | gridtools clusters volumes adjmat generic setup multicolvar core symfunc bias vatom |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | EMMI DISTANCES MOLINFO BIASVALUE PRINT WHOLEMOLECULES GROUP CONVERT_TO_FES HISTOGRAM READ DUMPGRID RMSD | gridtools generic isdb multicolvar colvar core bias |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | RESTART PRINT FIT_TO_TEMPLATE CENTER DISTANCE METAD | generic setup colvar bias vatom |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | RESTART DISTANCES PRINT CENTER GROUP COORDINATION DISTANCE WHOLEMOLECULES | generic setup multicolvar colvar core vatom |
| 20.010 | Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations | materials | water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling | Pablo Piaggi | RESTART Q6 BF_LEGENDRE VOLUME PRINT UPPER_WALLS OPT_AVERAGED_SGD TD_WELLTEMPERED VES_LINEAR_EXPANSION OPT_DUMMY ENVIRONMENTSIMILARITY MATHEVAL | function ves generic setup envsim colvar symfunc bias |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | PATHMSD PRINT UPPER_WALLS LOWER_WALLS WHOLEMOLECULES METAD | generic bias colvar |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | ENERGY PRINT UPPER_WALLS FLUSH COMBINE DISTANCE LOWER_WALLS UNITS METAD | generic setup function bias colvar |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | MORE_THAN FCCUBIC CENTER FIND_CONTOUR_SURFACE GROUP UNITS FOURIER_TRANSFORM DUMPGRID MULTICOLVARDENS | gridtools fourier setup contour function core symfunc vatom |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | PRINT UPPER_WALLS LOWER_WALLS DISTANCE WHOLEMOLECULES COM METAD | generic bias vatom colvar |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | TORSION DRR PRINT | generic drr colvar |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | POSITION PRINT ENDPLUMED UPPER_WALLS REWEIGHT_METAD FLUSH FIT_TO_TEMPLATE READ GROUP COORDINATION CONVERT_TO_FES WRAPAROUND HISTOGRAM WHOLEMOLECULES DUMPGRID COM MATHEVAL METAD | gridtools function generic colvar core bias vatom |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | MOLINFO BIASVALUE INCLUDE PRINT RESTRAINT ENDPLUMED UPPER_WALLS SAXS CENTER GROUP DISTANCE STATS WHOLEMOLECULES RMSD | function generic isdb colvar core bias vatom |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | ERMSD MOLINFO DISTANCES PRINT INCLUDE UPPER_WALLS FLUSH COMBINE DISTANCE LOWER_WALLS ANGLE RANDOM_EXCHANGES METAD | generic multicolvar function bias colvar |
| 26.000 | OPES simulations of disordered proteins | bio | OPES, IDPs | Julian Streit | RESTART ECV_MULTITHERMAL OPES_EXPANDED ENERGY PRINT | colvar setup opes generic |
| 25.014 | Atomic resolution ensembles of intrinsically disordered proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | GROUP BAIES PRINT BIASVALUE | isdb core generic bias |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | PYTORCH_MODEL CUSTOM WHOLEMOLECULES COMBINE MOLINFO MATHEVAL DISTANCE OPES_METAD GROUP TORSION ENDPLUMED COMMITTOR ENERGY PRINT | pytorch opes colvar function generic core |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | ABMD PATHMSD UNITS ENDPLUMED UPPER_WALLS PRINT | generic colvar setup bias |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | DISTANCES WHOLEMOLECULES LOWER_WALLS COMBINE MOLINFO POSITION GYRATION METAD MATHEVAL DISTANCE SORT GROUP GHOST UPPER_WALLS CENTER PUCKERING PRINT | multicolvar vatom colvar function generic core bias |
| 24.020 | Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics | bio | LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning | Ziyue Zou, Dedi Wang, Pratyush Tiwary | METAD GROUP TORSION COMMITTOR PRINT LOAD | setup colvar generic core bias |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | COORDINATION WHOLEMOLECULES GYRATION ALPHABETA DISTANCE MOVINGRESTRAINT TORSION INCLUDE PRINT COM | vatom multicolvar colvar generic bias |
| 23.035 | An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors | bio | G protein coupled receptor, peptide ligands, metadynamics, multiple-walker | Timothy Clark | WHOLEMOLECULES LOWER_WALLS METAD MATHEVAL DISTANCE CONSTANT BIASVALUE UPPER_WALLS CENTER PRINT | vatom colvar function generic bias |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | METAD GROUP INCLUDE CENTER COORDINATIONNUMBER PRINT LOAD | setup vatom symfunc generic core bias |
| 23.017 | How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques | bio | enzymatic reaction discovery, reaction mechanism, catalysis, ligand-binding modes, water, alpha-amylase, sugar, QM/MM MD, OPES, OPES explore, graph CV, machine learning, Deep TDA CV, path CV | Sudip Das | PYTORCH_MODEL COORDINATION CUSTOM WHOLEMOLECULES LOWER_WALLS OPES_METAD_EXPLORE DISTANCE FIXEDATOM OPES_METAD GROUP UNITS TORSION UPPER_WALLS FIT_TO_TEMPLATE CENTER PRINT PATH | pytorch opes setup vatom colvar function generic mapping core bias |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | TORSION METAD PRINT | generic colvar bias |
| 22.032 | Reciprocal barrier restraint. Application to path-meta-eABF | methods | restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC | Istvan Kolossvary | CUSTOM FLUSH PATHMSD METAD DRR BIASVALUE PRINT | colvar function drr generic bias |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | COORDINATION WHOLEMOLECULES LOWER_WALLS FLUSH GYRATION METAD GROUP UPPER_WALLS PRINT | colvar core generic bias |
| 22.027 | Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain | Max Bonomi | RMSD PRINT | colvar generic |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | RESTART PBMETAD WHOLEMOLECULES MOLINFO ANTIBETARMSD ALPHABETA TORSION ALPHARMSD PRINT COM | setup multicolvar vatom colvar secondarystructure generic bias |
| 22.023 | Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy | bio | CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble | Faidon Brotzakis | RESTART COORDINATION PBMETAD WHOLEMOLECULES MOLINFO RMSD EMMI GROUP TORSION BIASVALUE UPPER_WALLS PRINT COM | setup isdb vatom colvar generic core bias |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | CUSTOM PBMETAD LOWER_WALLS OPES_METAD_EXPLORE POSITION ECV_MULTITHERMAL METAD OPES_METAD TORSION ECV_UMBRELLAS_FILE ENDPLUMED OPES_EXPANDED UNITS BIASVALUE ENERGY PRINT UPPER_WALLS | opes setup colvar function generic bias |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | CENTER PRINT DISTANCE | vatom colvar generic |
| 21.040 | A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms | bio | EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference | Faidon Brotzakis | RESTART WHOLEMOLECULES MOLINFO EMMI DISTANCE GROUP BIASVALUE UPPER_WALLS PRINT COM | setup isdb vatom colvar generic core bias |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | WHOLEMOLECULES MOLINFO ECV_MULTITHERMAL Q6 GROUP TORSION ENDPLUMED LOAD PYTORCH_MODEL VOLUME FLUSH RMSD INCLUDE CONTACTMAP OPES_METAD UNITS ENERGY PRINT COMBINE DISTANCE OPES_EXPANDED ENVIRONMENTSIMILARITY | opes setup pytorch envsim colvar function symfunc generic core |
| 21.034 | Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics | bio | reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics | Dongdong Wang | RANDOM_EXCHANGES PBMETAD METAD TORSION INCLUDE ENDPLUMED PRINT | colvar generic bias |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | REWEIGHT_METAD FLUSH DUMPGRID METAD MOVINGRESTRAINT UNITS HISTOGRAM UPPER_WALLS COMMITTOR COORDINATIONNUMBER PRINT LOAD CONVERT_TO_FES | setup symfunc generic gridtools bias |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | PYTORCH_MODEL LOWER_WALLS FLUSH MATHEVAL OPES_METAD GROUP UPPER_WALLS PRINT LOAD | pytorch opes setup function generic core bias |
| 21.004 | Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy | bio | machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding | Dorothea Gobbo | RESTART WHOLEMOLECULES LOWER_WALLS PATHMSD METAD UPPER_WALLS PRINT | colvar setup generic bias |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | COORDINATION PBMETAD WHOLEMOLECULES CENTER PRINT | generic colvar bias vatom |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | DISTANCES LOWER_WALLS COMBINE DISTANCE GROUP TORSION UNITS UPPER_WALLS ENERGY PRINT LOAD | setup multicolvar colvar function generic core bias |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | LOWER_WALLS VOLUME METAD MATHEVAL UPPER_WALLS ENERGY PRINT CELL | generic colvar function bias |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | RESTART WHOLEMOLECULES COMBINE MOLINFO METAD RMSD DISTANCE TORSION UPPER_WALLS PRINT | setup colvar function generic bias |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | PYTORCH_MODEL LOWER_WALLS FLUSH MATHEVAL OPES_METAD DISTANCE GROUP TORSION UNITS ENDPLUMED UPPER_WALLS PRINT LOAD COM | pytorch opes setup vatom colvar function generic core bias |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | COORDINATION WHOLEMOLECULES LOWER_WALLS DISTANCE RESTRAINT ENDPLUMED | colvar generic bias |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | EXTERNAL REWEIGHT_METAD DUMPGRID METAD MATHEVAL DISTANCE TORSION BIASVALUE HISTOGRAM REWEIGHT_BIAS COMMITTOR PRINT READ CONVERT_TO_FES | colvar function generic gridtools bias |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | LOWER_WALLS METAD DISTANCE COMMITTOR TORSION UPPER_WALLS CENTER PRINT | generic colvar bias vatom |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | RESTART VES_DELTA_F POSITION METAD TORSION UNITS ENDPLUMED ENERGY PRINT LOAD | setup ves colvar generic bias |
| 26.006 | Metadynamics simulations of buried phosphorylation sites and proline isomerisation | bio | metadynamics | Julian Streit | WHOLEMOLECULES COORDINATION PRINT MOLINFO METAD TORSION | bias generic colvar |
| 26.001 | Molecular simulations Alx riboswitch | bio | RNA, riboswitch | Giovanni Bussi | MOVINGRESTRAINT MATHEVAL DISTANCE PRINT MOLINFO RESTRAINT ERMSD | bias function generic colvar |
| 25.027 | Enhanced-sampling MD simulations of a protein-peptide complex integrating SAXS and XL-MS experimental information | bio | steered MD, metadynamics, SAXS, XL-MS, ensemble reconstruction | Mattia Bernetti | GROUP GYRATION SAXS CENTER MOVINGRESTRAINT DISTANCE UPPER_WALLS WHOLEMOLECULES PRINT MOLINFO METAD INCLUDE | vatom core bias colvar generic isdb |
| 25.022 | Imidazole Diffusion in SALEM-2 MOF | materials | OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials | Sudheesh Kumar Ethirajan | CENTER GROUP ENDPLUMED DISTANCE WHOLEMOLECULES PROJECTION_ON_AXIS UNITS DISTANCES OPES_METAD PRINT MOLINFO | vatom core setup multicolvar opes colvar generic |
| 25.016 | Advancing in silico drug design with Bayesian refinement of AlphaFold models | bio | bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment | Samiran Sen | GROUP PRINT BIASVALUE BAIES | bias generic isdb core |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | ECV_MULTITHERMAL RESTART ERMSD OPES_EXPANDED COMBINE VOLUME COORDINATION PRINT MOLINFO PYTORCH_MODEL OPES_METAD_EXPLORE ENERGY | pytorch setup opes colvar function generic |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | RESTART PRINT MOLINFO PUCKERING METAD TORSION | bias generic setup colvar |
| 24.022 | Integrating Path Sampling with Enhanced Sampling for Rare-event Kinetics | methods | OPES Flooding, Weighted Ensemble, Metadynamics, Kinetics, Infrequent Metadynamics, Integrated Sampling | Dhiman Ray | ENDPLUMED DISTANCE COMBINE MOLINFO TORSION COMMITTOR GROUP CENTER FIXEDATOM UPPER_WALLS RMSD CONTACTMAP WHOLEMOLECULES COORDINATION OPES_METAD CUSTOM PRINT MATHEVAL FIT_TO_TEMPLATE ANGLE METAD | vatom core bias opes colvar function generic |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | CLUSTER_PROPERTIES CONTACT_MATRIX COORDINATIONNUMBER UPPER_WALLS CLUSTER_NATOMS UNITS PRINT DFSCLUSTERING METAD | adjmat symfunc bias setup generic clusters |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | LOAD GROUP RESTART PRINT METAD INCLUDE | bias generic setup core |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | CENTER DISTANCE COMBINE DUMPMASSCHARGE UPPER_WALLS FIXEDATOM PRINT MOLINFO RESTRAINT METAD | vatom bias colvar function generic |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | Q6 MATHEVAL Q4 COORDINATIONNUMBER COMBINE VOLUME PRINT METAD ENERGY | symfunc bias colvar function generic |
| 23.013 | Path meta-eABF simulation of large scale conformational change in STING protein | methods | meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint | Istvan Kolossvary | UPPER_WALLS BIASVALUE FLUSH UNITS CUSTOM PATHMSD PRINT TIME LOWER_WALLS METAD DRR | bias setup colvar function generic drr |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | PAIRENTROPY Q6 Q4 UPPER_WALLS VOLUME PIV CUSTOM UNITS FUNCPATHMSD PRINT RESTRAINT LOCAL_AVERAGE METAD ENERGY | piv symfunc bias setup colvar function gridtools generic |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | UNITS CUSTOM COORDINATION PRINT PYTORCH_MODEL OPES_METAD_EXPLORE | pytorch setup opes colvar function generic |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | CONVERT_TO_FES HISTOGRAM PRINT MOLINFO PUCKERING DUMPGRID READ METAD TORSION | bias generic gridtools colvar |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | LOAD GROUP WHOLEMOLECULES BIASVALUE PRINT MOLINFO EMMIVOX | core bias setup generic isdb |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | GROUP MATHEVAL DISTANCE COMBINE WHOLEMOLECULES UPPER_WALLS FLUSH UNITS COORDINATION BRIDGE DISTANCES PRINT RMSD FIT_TO_TEMPLATE ANGLE LOWER_WALLS METAD | adjmat core bias setup multicolvar colvar function generic |
| 22.007 | Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy | bio | metadynamics, well-tempered, protein-protein interactions, disordered proteins, mutations autophagy | Elena Papaleo | DISTANCE WHOLEMOLECULES UPPER_WALLS FLUSH COORDINATION ALPHABETA PRINT MOLINFO ALPHARMSD ANGLE METAD TORSION | bias multicolvar colvar generic secondarystructure |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | CONVERT_TO_FES GYRATION GROUP COMBINE DISTANCES REWEIGHT_BIAS METAD PRINT DUMPGRID HISTOGRAM INCLUDE COM | vatom core bias multicolvar colvar function gridtools generic |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | LOAD GROUP DISTANCE FIXEDATOM PRINT RESTRAINT | vatom core bias setup colvar generic |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | DISTANCE WHOLEMOLECULES UPPER_WALLS UNITS PRINT LOWER_WALLS METAD COM | vatom bias setup colvar generic |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | CONVERT_TO_FES ENDPLUMED DISTANCE HISTOGRAM GROUP FIXEDATOM UPPER_WALLS RMSD READ COM WHOLEMOLECULES FLUSH COORDINATION PRINT DUMPGRID REWEIGHT_METAD POSITION MATHEVAL METAD | vatom core bias colvar function generic gridtools |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | LOAD ENDPLUMED VOLUME MOLINFO TORSION Q6 ECV_MULTITHERMAL UPPER_WALLS ECV_UMBRELLAS_LINE RMSD ENERGY OPES_EXPANDED ECV_LINEAR WHOLEMOLECULES ENVIRONMENTSIMILARITY UNITS CUSTOM PRINT POSITION ECV_MULTITHERMAL_MULTIBARIC MATHEVAL | symfunc bias setup opes colvar envsim function generic |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | GROUP GYRATION MATHEVAL DISTANCE BIASVALUE UNITS PRINT FISST RESTRAINT ENERGY | core bias setup fisst colvar function generic |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | LOAD GROUP DUMPATOMS WHOLEMOLECULES BIASVALUE PRINT MOLINFO EMMIVOX | core bias setup generic isdb |
| 19.081 | Calculation of phase diagrams in the multithermal-multibaric ensemble | methods | VES, variationally enhanced sampling, multithermal-multibaric, energy, Wang Landau, RefCV, kernel, bcc, fcc, sodium, aluminum | Pablo Piaggi | LOAD CONVERT_TO_FES OPT_AVERAGED_SGD COMBINE VOLUME HISTOGRAM OPT_DUMMY Q6 TD_WELLTEMPERED UPPER_WALLS LOWER_WALLS READ ENERGY TD_MULTITHERMAL_MULTIBARIC REWEIGHT_TEMP_PRESS REWEIGHT_BIAS PRINT DUMPGRID MATHEVAL RESTART BF_LEGENDRE CELL VES_LINEAR_EXPANSION | symfunc bias setup colvar ves function gridtools generic |
| 19.073 | On the role of enthalpic and entropic contributions on the conformational free energy landscape of MIL-101(Cr) building units | materials | metadynamics, MOF, MIL101Cr, conformational | Matteo Salvalaglio | GYRATION ENDPLUMED COORDINATIONNUMBER UPPER_WALLS DISTANCES PRINT LOWER_WALLS METAD ENERGY | symfunc bias multicolvar colvar generic |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | RESTART UPPER_WALLS UNITS PATHMSD PRINT LOWER_WALLS METAD | bias generic setup colvar |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | GYRATION WHOLEMOLECULES PRINT METAD ENERGY | bias generic colvar |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | LOAD Q6 ENDPLUMED ENVIRONMENTSIMILARITY UNITS PRINT ENERGY POSITION TORSION | symfunc setup colvar envsim generic |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_OPTIMIZER_BIAS UNITS MAZE_SIMULATED_ANNEALING PRINT POSITION MAZE_LOSS | generic maze setup colvar |
| 19.041 | Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces | bio | metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption | Jim Pfaendtner | DISTANCE UPPER_WALLS PRINT METAD ENERGY COM | bias generic vatom colvar |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | GYRATION ENDPLUMED WHOLEMOLECULES PRINT MOLINFO ALPHARMSD METAD ENERGY | bias generic secondarystructure colvar |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | GROUP WHOLEMOLECULES RDC CS2BACKBONE PRINT MOLINFO METAINFERENCE | generic isdb core |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | GROUP BIASVALUE EMMI PRINT MOLINFO | bias generic isdb core |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | GROUP BIASVALUE EMMI PRINT MOLINFO | bias generic isdb core |
| 26.004 | Resolving the ambiguous binding site of quercetin at the calcineurin subunit junction using funnel metadynamics with deep learning collective variables | bio | metadynamics, funnel metadynamics, DeepTICA | Jason Loo | PRINT MATHEVAL ENERGY PYTORCH_MODEL LOWER_WALLS RMSD WRAPAROUND UPPER_WALLS METAD FUNNEL_PS FUNNEL GROUP WHOLEMOLECULES COORDINATION COM DISTANCE | core bias pytorch funnel generic function colvar vatom |
| 25.023 | Molecular simulations of Tau-protein oligomers | bio | metadynamics, proteins, aggregation | Giovanni Bussi | PRINT RESTRAINT CONVERT_TO_FES CONTACTMAP FLUSH RMSD RESTART METAD REWEIGHT_BIAS HISTOGRAM DUMPGRID CUSTOM | bias gridtools generic function colvar setup |
| 25.017 | Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity | bio | EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase | Samuel Hoff | PRINT MOLINFO BIASVALUE EMMIVOX GROUP WHOLEMOLECULES | core generic bias isdb |
| 25.015 | Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY | materials | Molecular crystal, Force Field, Collective Variable | Pradip Si and Omar Valsson | PRINT SMAC TORSIONS DISTANCES DUMPMULTICOLVAR | multicolvar generic symfunc |
| 25.006 | Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations | methods | Enhanced sampling, Atomistic simulations, Conformational ensemble, PROTACs, Targeted Protein Degradation, Chamelonic molecules | Shikshya Bhusal, Omar Valsson | PRINT MOLINFO DUMPATOMS ENERGY TORSION INCLUDE PBMETAD GYRATION DISTANCE CENTER RESTART VOLUME UPDATE_IF READ WHOLEMOLECULES | setup bias generic colvar vatom |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | METAINFERENCE MOLINFO PRINT STATS FLUSH DISTANCE RDC GROUP ALPHABETA ENSEMBLE WHOLEMOLECULES | core multicolvar generic function colvar isdb |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | PRINT UNITS TORSION METAD GROUP | core bias generic colvar setup |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | CONVERT_TO_FES CONTACTMAP RMSD WRAPAROUND COORDINATION PATH WHOLEMOLECULES FIXEDATOM FLUSH UPPER_WALLS METAD GROUP DUMPGRID READ PRINT INCLUDE FIT_TO_TEMPLATE REWEIGHT_METAD COMMITTOR DISTANCE MOLINFO MATHEVAL ENDPLUMED HISTOGRAM COM | core mapping bias gridtools generic function colvar vatom |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | PRINT UNITS FLUSH POSITION DISTANCE DISTANCES CENTER METAD GROUP COM CUSTOM WHOLEMOLECULES | vatom core multicolvar bias generic function colvar setup |
| 23.031 | Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN | bio | RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites | Max Bonomi | PRINT MOLINFO SHADOW POSITION FIT_TO_TEMPLATE WRAPAROUND UPPER_WALLS CENTER DISTANCES METAD GROUP WHOLEMOLECULES | core isdb multicolvar bias generic colvar vatom |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | PRINT PBMETAD LOAD | generic bias setup |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | PRINT MATHEVAL BIASVALUE CONSTANT PBMETAD WHOLEMOLECULES ANGLE DISTANCE | colvar generic function bias |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | PRINT MOLINFO OPES_METAD_EXPLORE ENERGY ECV_MULTITHERMAL TORSION METAD ENDPLUMED OPES_EXPANDED DISTANCE | bias opes generic colvar |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | PRINT RESTRAINT TORSION INCLUDE PBMETAD GYRATION COORDINATION COM WHOLEMOLECULES | colvar generic bias vatom |
| 23.003 | Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations | methods | metadynamics, alchemical variable, alchemical free energy calculations | Wei-Tse Hsu | PRINT TORSION EXTRACV METAD READ | bias generic colvar |
| 22.035 | Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties | bio | intrinsically disordered proteins, parallel bias metadynamics, protein | Kresten Lindorff-Larsen | MOLINFO TORSION PBMETAD GYRATION WHOLEMOLECULES | bias generic colvar |
| 22.020 | Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA | bio | RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics | Weiwei He | PRINT TORSION DISTANCE METAD GROUP COM WHOLEMOLECULES | core bias generic colvar vatom |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | PRINT LOWER_WALLS DISTANCE UPPER_WALLS METAD FUNNEL_PS FUNNEL PATHMSD COM WHOLEMOLECULES | bias funnel generic colvar vatom |
| 22.001 | Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials | methods | enhanced sampling, variationally enhanced sampling, ves, metadynamics, bias representation, wavelets, adam | Benjamin Pampel | VES_OUTPUT_BASISFUNCTIONS BF_WAVELETS COORDINATION VES_LINEAR_EXPANSION ENERGY FLUSH TD_UNIFORM UPPER_WALLS METAD PRINT INCLUDE POSITION BF_GAUSSIANS OPT_AVERAGED_SGD DISTANCE BF_CHEBYSHEV UNITS BF_LEGENDRE TD_WELLTEMPERED OPT_ADAM BF_CUBIC_B_SPLINES | ves bias generic colvar setup |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | COORDINATION LOAD WHOLEMOLECULES FIXEDATOM TORSION PYTORCH_MODEL OPES_METAD LOWER_WALLS DISTANCES UPPER_WALLS GROUP PRINT FIT_TO_TEMPLATE DISTANCE MATHEVAL UNITS CENTER ENDPLUMED ANGLE | setup core multicolvar opes bias pytorch generic function colvar vatom |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | PRINT LOWER_WALLS DISTANCE UPPER_WALLS | colvar generic bias |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | PRINT MATHEVAL TORSIONS KDE COM DISTANCE | multicolvar gridtools generic function colvar vatom |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | PRINT RESTRAINT CONVERT_TO_FES REWEIGHT_METAD METAD HISTOGRAM DUMPGRID MULTI_RMSD | colvar generic bias gridtools |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | CONVERT_TO_FES PAIRENTROPY DENSITY COORDINATION LOAD ENERGY FLUSH LOWER_WALLS UPPER_WALLS METAD Q6 DUMPGRID PRINT CONTACT_MATRIX REWEIGHT_METAD REWEIGHT_BIAS COORDINATIONNUMBER DISTANCE UNITS CENTER SPRINT VOLUME COMBINE LOCAL_AVERAGE HISTOGRAM | volumes vatom sprint symfunc adjmat bias gridtools generic function colvar setup |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | METAINFERENCE MOLINFO PRINT SAXS TORSION STATS FLUSH PBMETAD GYRATION DISTANCE CENTER ALPHABETA ENSEMBLE WHOLEMOLECULES | vatom multicolvar bias generic function colvar isdb |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | PRINT CONVERT_TO_FES UPPER_WALLS RESTART METAD DISTANCE_FROM_CONTOUR REWEIGHT_BIAS COMBINE HISTOGRAM DUMPGRID READ | contour bias gridtools generic function setup |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | PRINT UNITS ENERGY FLUSH UPPER_WALLS METAD COMBINE DISTANCE | bias generic function colvar setup |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | PRINT FUNCPATHMSD LOWER_WALLS UPPER_WALLS METAD CELL PIV | bias piv generic function colvar |
| 25.021 | All You Need Is Water. Converging Ligand Binding Simulations with Hydration Collective Variables | bio | OPES Explore, ligand binding, binding free energy, water, hydration CVs, SAMPL challenge, host-guest | Valerio Rizzi | UPPER_WALLS WHOLEMOLECULES ENERGY ANGLE GROUP FIT_TO_TEMPLATE FIXEDATOM OPES_METAD_EXPLORE CENTER MATHEVAL PRINT COORDINATION DISTANCE | vatom bias generic colvar function core opes |
| 25.019 | The Arch from the Stones. Understanding Protein Folding Energy Landscapes via Bio-inspired Collective Variables | bio | protein folding, OPES, OneOPES, binding free energy | Valerio Rizzi | COMBINE ENERGY GHOST GROUP MOLINFO OPES_METAD_EXPLORE OPES_EXPANDED CENTER ECV_MULTITHERMAL DISTANCE PRINT COORDINATION RMSD CUSTOM | vatom generic opes colvar core function |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | UPPER_WALLS REWEIGHT_METAD CUSTOM GROUP READ DUMPGRID FLUSH RESTART METAD HISTOGRAM PRINT COORDINATION DISTANCE | setup gridtools colvar generic bias core function |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | POSITION PRINT UNITS RESTRAINT | setup generic bias colvar |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | LOWER_WALLS UNITS BIASVALUE CUSTOM TORSION WHOLEMOLECULES ENERGY GROUP MOLINFO LOAD DISTANCE POSITION ENDPLUMED CELL COORDINATION UPPER_WALLS INCLUDE MATHEVAL PRINT RMSD | setup bias generic colvar core function |
| 24.001 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | bio | OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis | Dhiman Ray | UPPER_WALLS COMBINE TORSION CUSTOM COMMITTOR LOWER_WALLS UNITS OPES_METAD FLUSH PRINT DISTANCE | setup bias generic opes colvar function |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | GROUP CONVERT_TO_FES COMMITTOR READ DUMPGRID METAD ENDPLUMED HISTOGRAM PRINT COORDINATION | gridtools bias generic colvar core |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | WHOLEMOLECULES REWEIGHT_METAD CONVERT_TO_FES MOLINFO READ DUMPGRID MATHEVAL METAD HISTOGRAM PRINT RMSD DISTANCE | gridtools bias generic colvar function |
| 22.011 | Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck | methods | metadynamics, membrane permeation, protein folding | Shams Mehdi | UPPER_WALLS ZANGLES COMBINE TORSION WHOLEMOLECULES MOLINFO COM LOWER_WALLS XANGLES MATHEVAL YANGLES METAD ALPHABETA DISTANCE PRINT CUSTOM | vatom multicolvar bias generic colvar function |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | TORSION COORDINATIONNUMBER COMMITTOR CENTER METAD ENDPLUMED PRINT DISTANCE | vatom colvar generic symfunc bias |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | COMBINE ERMSD WHOLEMOLECULES MOLINFO METAD BIASVALUE PRINT COORDINATION | generic bias function colvar |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | COMBINE ENERGY VES_LINEAR_EXPANSION BF_LEGENDRE RESTART PAIRENTROPY METAD OPT_AVERAGED_SGD TD_WELLTEMPERED LOAD PRINT VOLUME | setup gridtools bias ves generic colvar function |
| 21.043 | Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes | chemistry | well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability | Huixia Lu | TORSION FIT_TO_TEMPLATE FIXEDATOM METAD PRINT | vatom generic bias colvar |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | PRINT RMSD DISTANCE | generic colvar |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | UPPER_WALLS COMBINE INCLUDE METAD MOVINGRESTRAINT CONSTANT PRINT RESTRAINT | generic function bias |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | WHOLEMOLECULES GROUP UNITS COORDINATION PBMETAD | setup colvar generic bias core |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | TORSION WHOLEMOLECULES MATHEVAL RESTART BIASVALUE CONSTANT PRINT PBMETAD | setup colvar generic bias function |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | UPPER_WALLS WHOLEMOLECULES REWEIGHT_METAD ENERGY GROUP MOLINFO LOWER_WALLS INCLUDE DUMPGRID RANDOM_EXCHANGES METAD HISTOGRAM PUCKERING PRINT COORDINATION DISTANCE | gridtools bias generic colvar core |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | UPPER_WALLS GROUP INCLUDE CENTER METAD LOAD PRINT VOLUME | setup vatom colvar generic bias core |
| 20.008 | Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol | chemistry | proton trasfer, metadynamics | Kevin Rossi | DISTANCES UNITS METAD PRINT COORDINATION CUSTOM | setup multicolvar bias generic colvar function |
| 20.001 | Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins | bio | metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals | Carlo Camilloni | UPPER_WALLS CS2BACKBONE WHOLEMOLECULES GROUP ANTIBETARMSD MOLINFO LOWER_WALLS FLUSH BIASVALUE ENDPLUMED ALPHABETA PRINT PBMETAD | multicolvar secondarystructure generic isdb bias core |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | COMBINE GROUP COORDINATIONNUMBER UNITS RESTART FLUSH METAD ENDPLUMED PRINT EXTERNAL | setup generic symfunc bias core function |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | GROUP INCLUDE CENTER ENDPLUMED PRINT DISTANCE | vatom generic core colvar |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | UPPER_WALLS UNITS METAD ENDPLUMED CELL PRINT FCCUBIC | setup bias generic symfunc colvar |
| 19.045 | Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water | materials | metadynamics, well-tempered, multiple walkers, LAMMPS | Marco De La Pierre | UPPER_WALLS POSITION GROUP LOWER_WALLS UNITS RESTART FLUSH METAD PRINT COORDINATION | setup bias generic colvar core |
| 25.025 | Enhanced Sampling of Ligand Binding Coupled to RNA Conformational Dynamics | bio | OPES, OPES Flooding , Metadynamics, RNA, Ligand binding, Free Energy, Kinetics, Funnel | Revanth Elangovan and Dhiman Ray | DISTANCE WRAPAROUND OPES_METAD RMSD COM WHOLEMOLECULES COORDINATION UPPER_WALLS TORSION COMMITTOR CENTER CUSTOM PRINT FUNNEL_PS LOWER_WALLS MATHEVAL GROUP ENDPLUMED FUNNEL METAD | generic colvar function funnel bias core opes vatom |
| 25.020 | Revealing Water-Mediated Activation Mechanisms in the Beta 1-Adrenergic Receptor via OneOPES-Enhanced Free Energy Landscapes | bio | OneOPES, GPCR, ADRB1, activation, microswitches, conformational changes, allostery | Valerio Rizzi | CUSTOM DISTANCE OPES_METAD_EXPLORE RMSD PRINT OPES_EXPANDED COORDINATION UPPER_WALLS PATHMSD LOWER_WALLS GROUP GHOST ENERGY CENTER ECV_MULTITHERMAL DISTANCES | generic colvar function bias core opes vatom multicolvar |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | DISTANCE PYTORCH_MODEL GYRATION PRINT RESTRAINT | generic colvar pytorch bias |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | DISTANCE ABMD FLUSH PRINT COM GROUP COMMITTOR WHOLEMOLECULES | generic colvar core bias vatom |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | DISTANCE OPES_METAD POSITION BIASVALUE RMSD UNITS INCLUDE FIT_TO_TEMPLATE COMBINE ENERGY WHOLEMOLECULES FLUSH COORDINATION UPPER_WALLS CENTER CUSTOM PYTORCH_MODEL PRINT LOWER_WALLS MATHEVAL GROUP OPES_METAD_EXPLORE ENDPLUMED CONTACTMAP METAD FIXEDATOM MOLINFO | generic colvar function pytorch bias core opes vatom setup |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | DISTANCE PBMETAD GYRATION FLUSH PRINT INCLUDE COORDINATION DIHCOR PARABETARMSD COMBINE ENDPLUMED GROUP TORSION MOLINFO WHOLEMOLECULES ALPHARMSD ANTIBETARMSD | generic colvar function secondarystructure bias core multicolvar |
| 24.014 | Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation | methods | data augmentation, geodesic interpolation, collective variables, protein folding | Juno Nam | PYTORCH_MODEL DRR FLUSH RMSD PRINT COORDINATION UPPER_WALLS LOWER_WALLS METAD WHOLEMOLECULES MOLINFO | generic colvar pytorch bias drr |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | WHOLEMOLECULES OPES_EXPANDED PRINT INCLUDE UPPER_WALLS CONTACTMAP ENERGY ECV_MULTITHERMAL MOLINFO | generic colvar opes bias |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | CUSTOM DISTANCE BIASVALUE UNITS PRINT | generic colvar function bias setup |
| 23.038 | Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor | bio | protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics | Timothy Clark | DISTANCE RMSD PRINT MATHEVAL METAD WHOLEMOLECULES MOLINFO | function generic colvar bias |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | LOCAL_AVERAGE RESTRAINT COORDINATIONNUMBER CLUSTER_NATOMS CONTACT_MATRIX UNITS PRINT CLUSTER_DISTRIBUTION AROUND DUMPGRID Q3 GROUP LOCAL_Q3 DENSITY HISTOGRAM LOAD FIXEDATOM DFSCLUSTERING | clusters generic adjmat gridtools bias core symfunc vatom setup volumes |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | CUSTOM DISTANCE VSTACK SKETCHMAP SKETCHMAP_PROJECTION COLLECT_FRAMES PRINT UPPER_WALLS LANDMARK_SELECT_FPS PATHMSD COM VORONOI METAD DISSIMILARITIES WHOLEMOLECULES TRANSPOSE | generic colvar function valtools bias landmarks matrixtools vatom dimred |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | DISTANCE PBMETAD GYRATION PRINT UPPER_WALLS COM | bias colvar vatom generic |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | CUSTOM DISTANCE OPES_METAD_EXPLORE PRINT COORDINATION UPPER_WALLS LOWER_WALLS COM METAD GROUP WHOLEMOLECULES CENTER | generic colvar function bias core opes vatom |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | OPES_EXPANDED PRINT INCLUDE UPPER_WALLS RESTART LOWER_WALLS ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY | generic bias envsim opes setup |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | DISTANCE ANGLE PRINT UPPER_WALLS LOWER_WALLS COM METAD WHOLEMOLECULES MOVINGRESTRAINT | generic colvar vatom bias |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | LOCAL_AVERAGE LOCAL_Q4 COORDINATIONNUMBER Q6 MFILTER_LESS CONTACT_MATRIX CLUSTER_NATOMS Q4 PRINT COMBINE LOCAL_Q6 GROUP MFILTER_MORE DFSCLUSTERING | clusters generic adjmat function core symfunc multicolvar |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | CUSTOM DISTANCE DRR BIASVALUE UNITS PRINT FLUSH COM METAD | generic colvar function bias vatom setup drr |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | CUSTOM RESTRAINT COORDINATIONNUMBER BIASVALUE UNITS FLUSH VOLUME PRINT UPPER_WALLS CONVERT_TO_FES DUMPGRID REWEIGHT_BIAS COMMITTOR HISTOGRAM LOAD ANN MOVINGRESTRAINT | generic colvar function gridtools bias symfunc annfunc setup |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | RMSD PRINT | generic colvar |
| 22.017 | Water regulates the residence time of Benzamidine in Trypsin | bio | ligand binding, water, opes, benzamidine trypsin, unbinding rates, machine learning, Deep-LDA, Deep-TICA | Narjes Ansari | CUSTOM DISTANCE PYTORCH_MODEL OPES_METAD RMSD PRINT FIT_TO_TEMPLATE COORDINATION UPPER_WALLS LOWER_WALLS MATHEVAL CENTER GROUP COMMITTOR WHOLEMOLECULES FIXEDATOM | generic colvar function pytorch bias core opes vatom |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | ANGLE DISTANCE WHOLEMOLECULES PYTORCH_MODEL FLUSH PRINT FIT_TO_TEMPLATE COORDINATION UPPER_WALLS ENDPLUMED MATHEVAL CENTER GROUP COMMITTOR LOAD ENERGY FIXEDATOM | generic colvar function pytorch bias core vatom setup |
| 21.048 | Enhancing ligand exploration within a channel pore and fenestrations using metadynamics | bio | well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug | Elaine Tao | CUSTOM DISTANCE UNITS PRINT UPPER_WALLS COM LOWER_WALLS METAD TORSION | generic colvar function bias vatom setup |
| 21.045 | QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP) | chemistry | metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange | Denis Maag | DISTANCE COORDINATIONNUMBER PRINT COORDINATION UPPER_WALLS COMBINE LOWER_WALLS METAD | generic colvar function bias symfunc |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | COORDINATIONNUMBER Q6 CLUSTER_NATOMS CONTACT_MATRIX PRINT CLUSTER_DISTRIBUTION COMBINE DUMPGRID LOCAL_Q6 MFILTER_MORE METAD GROUP HISTOGRAM INSPHERE FIXEDATOM DFSCLUSTERING | clusters generic adjmat function gridtools bias core symfunc vatom multicolvar volumes |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | DISTANCE PBMETAD GYRATION PRINT UPPER_WALLS COM MOLINFO | bias colvar vatom generic |
| 21.015 | Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin | bio | metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module | Gaston Courtade | PRINT COORDINATION RESTART MATHEVAL METAD REWEIGHT_BIAS RESTRAINT WHOLEMOLECULES CENTER POSITION | generic colvar function bias vatom setup |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | PBMETAD SAXS STATS GYRATION ALPHABETA BIASVALUE PRINT ENSEMBLE CONTACTMAP METAD TORSION MOLINFO WHOLEMOLECULES CENTER ANTIBETARMSD | generic colvar function secondarystructure bias isdb vatom multicolvar |
| 21.002 | Phase equilibrium of water with hexagonal and cubic ice using the SCAN functional | materials | ice, water, SCAN, OPES, VES, multithermal, crystallization, environment similarity, refcv, reweighting | Pablo Piaggi | BF_LEGENDRE VES_LINEAR_EXPANSION Q6 ECV_MULTITHERMAL_MULTIBARIC OPES_EXPANDED PRINT VOLUME OPT_AVERAGED_SGD UPPER_WALLS RESTART ECV_UMBRELLAS_LINE MATHEVAL ENVIRONMENTSIMILARITY TD_UNIFORM ENERGY | ves generic colvar function bias envsim symfunc opes setup |
| 20.030 | Converging experimental and computational views of the knotting mechanism of the smallest knotted protein | bio | phi-values, transition state, knotted proteins | Cristina Paissoni | PRINT COORDINATION COMBINE RESTRAINT WHOLEMOLECULES STATS MOLINFO | function generic colvar bias |
| 20.027 | Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery | bio | SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery | Khaled Abdel-Maksoud | DISTANCE METAD TORSION PRINT | bias colvar generic |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | METAD TORSION PRINT | bias colvar generic |
| 20.014 | amyloid beta small molecule interaction | bio | intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta | Gabriella Heller | INCLUDE COMBINE METAINFERENCE WHOLEMOLECULES PARABETARMSD ALPHARMSD ANTIBETARMSD PBMETAD GYRATION FLUSH DIHCOR COORDINATION TORSION CS2BACKBONE STATS ENSEMBLE PRINT GROUP ENDPLUMED MOLINFO | generic colvar function secondarystructure bias core isdb multicolvar |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | DISTANCE WHOLEMOLECULES RMSD PRINT UPPER_WALLS COMBINE LOWER_WALLS MATHEVAL METAD ENERGY CENTER MOLINFO | generic colvar function bias vatom |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | UNITS PRINT MAZE_LOSS MAZE_SIMULATED_ANNEALING MAZE_OPTIMIZER_BIAS POSITION | generic colvar setup maze |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | DISTANCE GYRATION PRINT UPPER_WALLS COM METAD ENERGY MOLINFO | generic colvar vatom bias |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | ANGLE SAXS PBMETAD ALPHABETA BIASVALUE PRINT INCLUDE COORDINATION ENSEMBLE COMBINE ENDPLUMED MATHEVAL CENTER GROUP WHOLEMOLECULES STATS MOLINFO | generic colvar function bias core isdb vatom multicolvar |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | DISTANCE RMSD PRINT FUNCPATHMSD ENDPLUMED COM CONTACTMAP METAD WHOLEMOLECULES | generic colvar function bias vatom |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | CONSTANT BIASVALUE INCLUDE MATHEVAL TORSION PUCKERING MOLINFO | function generic colvar bias |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | PBMETAD DISTANCE GYRATION ALPHABETA PRINT INCLUDE COORDINATION METAINFERENCE GROUP CS2BACKBONE WHOLEMOLECULES CENTER MOLINFO | generic colvar bias core isdb vatom multicolvar |