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 |
---|---|---|---|---|---|---|
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 | TORSION DISTANCE COORDINATION ENERGY ECV_MULTITHERMAL OPES_EXPANDED CUSTOM GROUP PRINT COMBINE OPES_METAD_EXPLORE RESTART | core function setup opes generic colvar |
24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | CONTACTMAP INCLUDE LOWER_WALLS ECV_MULTITHERMAL MOLINFO WHOLEMOLECULES OPES_METAD_EXPLORE TORSION WRAPAROUND PROJECTION_ON_AXIS CUSTOM COM PRINT RESTART CONSTANT METAD COORDINATION GROUP UPPER_WALLS BIASVALUE ENERGY OPES_EXPANDED MATHEVAL RMSD | core bias function setup opes vatom generic colvar |
24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | CONTACTMAP INCLUDE ENERGY ECV_MULTITHERMAL OPES_EXPANDED MOLINFO PRINT WHOLEMOLECULES UPPER_WALLS | generic colvar opes bias |
23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | AROUND CLUSTER_DISTRIBUTION Q3 LOCAL_AVERAGE COORDINATIONNUMBER CLUSTER_NATOMS HISTOGRAM UNITS DENSITY PRINT CONTACT_MATRIX RESTRAINT DUMPGRID FIXEDATOM DFSCLUSTERING LOAD GROUP LOCAL_Q3 | core clusters symfunc bias setup adjmat vatom gridtools volumes generic |
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 setup bias |
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 | FLUSH BIASVALUE METAD UNITS TIME DRR LOWER_WALLS CUSTOM PATHMSD PRINT UPPER_WALLS | bias drr function setup generic colvar |
23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | METAD TORSION DISTANCE ENERGY ECV_MULTITHERMAL OPES_EXPANDED MOLINFO PRINT ENDPLUMED OPES_METAD_EXPLORE | generic colvar opes bias |
23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | TORSION GYRATION MOLINFO PBMETAD GROUP PRINT WHOLEMOLECULES | core generic colvar bias |
23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | REWEIGHT_METAD METAD HISTOGRAM READ PRINT DISTANCE DUMPGRID CONVERT_TO_FES MOLINFO MATHEVAL RMSD WHOLEMOLECULES | bias function gridtools generic colvar |
22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | ECV_UMBRELLAS_LINE CONTACTMAP ENERGY ECV_MULTITHERMAL OPES_EXPANDED PRINT WHOLEMOLECULES | generic colvar opes |
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 | TORSION GYRATION MOLINFO PBMETAD WHOLEMOLECULES | generic colvar bias |
22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | FLUSH METAD COORDINATION LOWER_WALLS GYRATION GROUP PRINT WHOLEMOLECULES UPPER_WALLS | core generic colvar 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 | BIASVALUE EMMI TORSION PRINT COORDINATION COM MOLINFO PBMETAD GROUP RMSD WHOLEMOLECULES UPPER_WALLS RESTART | core bias setup vatom generic colvar isdb |
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 | PRINT FIT_TO_TEMPLATE COORDINATION DISTANCE PYTORCH_MODEL LOWER_WALLS OPES_METAD FIXEDATOM CENTER COMMITTOR MATHEVAL CUSTOM GROUP RMSD WHOLEMOLECULES UPPER_WALLS | core pytorch bias function opes vatom generic colvar |
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 | METAD UNITS TORSION DISTANCE LOWER_WALLS CUSTOM COM PRINT UPPER_WALLS | bias function setup vatom generic colvar |
21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | DISTANCE GYRATION MOLINFO PBMETAD COM PRINT UPPER_WALLS | vatom generic 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 | FLUSH TORSION ENERGY MOLINFO PRINT EXTERNAL RESTART | setup generic colvar bias |
21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | DISTANCE WHOLEMOLECULES FLUSH READ CONVERT_TO_FES COM PRINT METAD HISTOGRAM COORDINATION FIXEDATOM GROUP UPPER_WALLS POSITION REWEIGHT_METAD DUMPGRID MATHEVAL RMSD ENDPLUMED | core bias function vatom gridtools generic colvar |
21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | SECONDARY_STRUCTURE_RMSD CONTACTMAP CONSTANT SUM ALPHABETA METAD TORSION MOLINFO LESS_THAN PBMETAD ALPHARMSD CUSTOM GROUP PRINT REWEIGHT_BIAS COMBINE WHOLEMOLECULES RESTART | multicolvar core bias function secondarystructure setup generic colvar |
21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | FLUSH BIASVALUE GYRATION MOLINFO EEFSOLV CENTER ALPHARMSD PBMETAD GROUP PRINT METAINFERENCE SAXS WHOLEMOLECULES | core bias secondarystructure vatom generic colvar isdb |
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 | TD_UNIFORM ONES DISTANCE_MATRIX Q6 COMBINE SPHERICAL_HARMONIC VOLUME ECV_UMBRELLAS_LINE CONTACT_MATRIX MORE_THAN VES_LINEAR_EXPANSION CUSTOM PRINT RESTART OPT_AVERAGED_SGD MEAN ENVIRONMENTSIMILARITY ECV_MULTITHERMAL_MULTIBARIC GROUP UPPER_WALLS SUM MATRIX_VECTOR_PRODUCT ENERGY OPES_EXPANDED MATHEVAL BF_LEGENDRE | core matrixtools symfunc bias function setup adjmat opes generic colvar ves envsim |
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 | RESTRAINT COORDINATION STATS MOLINFO PRINT COMBINE WHOLEMOLECULES | function generic colvar bias |
20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | ENSEMBLE BIASVALUE INCLUDE RESTRAINT DISTANCE STATS MOLINFO CENTER GROUP PRINT SAXS WHOLEMOLECULES | core bias function vatom generic colvar isdb |
20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | METAD FIT_TO_TEMPLATE DISTANCE CENTER PRINT RESTART | bias setup vatom generic colvar |
20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | REWEIGHT_METAD CONSTANT METAD RESTRAINT HISTOGRAM PRINT DUMPGRID CONVERT_TO_FES CUSTOM RMSD_VECTOR CONCATENATE COMBINE MULTI_RMSD WHOLEMOLECULES POSITION | bias valtools function gridtools generic colvar |
20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | DIHCOR CONSTANT SUM INCLUDE ALPHABETA TORSION COORDINATION GYRATION MOLINFO PBMETAD CUSTOM DIHEDRAL_CORRELATION PRINT COMBINE WHOLEMOLECULES | multicolvar bias function generic colvar |
20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | VOLUME METAD CELL ENERGY LOWER_WALLS MATHEVAL PRINT UPPER_WALLS | function generic colvar bias |
20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | BIASVALUE EMMIVOX MOLINFO LOAD GROUP PRINT DUMPATOMS WHOLEMOLECULES | core bias setup generic isdb |
20.013 | Improving accuracy of biased Alchemistic simulations | methods | flying Gaussian method, Alchemistic simulations, thermodynamic integration, reweighting | Vojtech Spiwok | PRINT TORSION METAD | generic colvar bias |
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 | CONTACTMAP DISTANCE LOWER_WALLS MOLINFO COMBINE WHOLEMOLECULES FLUSH READ CONVERT_TO_FES COM PRINT FUNCPATHMSD METAD ABMD HISTOGRAM UPPER_WALLS REWEIGHT_METAD DUMPGRID ENDPLUMED | bias function vatom gridtools generic colvar |
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 | METAD MOLINFO PATHMSD GROUP PRINT WHOLEMOLECULES UPPER_WALLS RESTART | core bias setup generic colvar |
19.078 | Iterative unbiasing of quasi-equilibrium sampling | methods | metadynamics, reweighting | Federico Giberti | COLLECT_FRAMES COORDINATIONNUMBER BIASVALUE METAD UNITS DISTANCE MATHEVAL PRINT REWEIGHT_BIAS DUMPATOMS | symfunc bias landmarks function setup generic colvar |
19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | METAD DISTANCE ENERGY GYRATION MOLINFO COM PRINT UPPER_WALLS | vatom generic colvar bias |
19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | METAD ENERGY GYRATION PRINT WHOLEMOLECULES | generic colvar bias |
19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | METAD HISTOGRAM READ DUMPGRID DISTANCE_FROM_CONTOUR CONVERT_TO_FES COMBINE PRINT REWEIGHT_BIAS UPPER_WALLS RESTART | bias function setup gridtools generic contour |
19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | CONSTANT METAD BIASVALUE DISTANCE LOWER_WALLS MATHEVAL COM PRINT WHOLEMOLECULES UPPER_WALLS | bias function vatom generic colvar |
19.047 | Close Structure | methods | metadynamics, RMSD, path collective variables, property map | Vojtech Spiwok | PRINT PROPERTYMAP WHOLEMOLECULES METAD | generic colvar bias |
19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | METAD COORDINATION ENERGY GROUP EXTERNAL | core colvar bias |
19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
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 | OPES_METAD UPPER_WALLS CUSTOM RMSD CONTACTMAP FIT_TO_TEMPLATE COMMITTOR MOLINFO CENTER FIXEDATOM COORDINATION ANGLE GROUP MATHEVAL ENDPLUMED DISTANCE METAD TORSION WHOLEMOLECULES COMBINE PRINT | core function vatom generic colvar opes bias |
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 | OPES_METAD LESS_THAN MOLINFO DISTANCE CUSTOM TORSION COORDINATION WHOLEMOLECULES COMBINE GYRATION ALPHARMSD SECONDARY_STRUCTURE_RMSD PRINT SUM | function generic colvar opes secondarystructure |
24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | GROUP COM CENTER METAD RESTART INCLUDE LOAD PRINT | core vatom generic setup 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 | ONES GROUP CONTACT_MATRIX UNITS OPES_METAD FLUSH UPPER_WALLS MATRIX_VECTOR_PRODUCT DISTANCE CENTER FIXEDATOM CUSTOM ZDISTANCES MEAN PRINT SUM COORDINATIONNUMBER | core symfunc adjmat vatom function generic multicolvar setup matrixtools colvar opes bias |
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 | LESS_THAN UPPER_WALLS MOLINFO DISTANCE FUNCPATHMSD METAD CONTACTMAP INCLUDE SECONDARY_STRUCTURE_RMSD ALPHARMSD PRINT SUM LOWER_WALLS PATHMSD | function generic colvar secondarystructure bias |
23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | GROUP COMMITTOR CONVERT_TO_FES ENDPLUMED HISTOGRAM DUMPGRID READ METAD COORDINATION PRINT | core generic colvar bias gridtools |
22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | OPES_METAD POSITION UNITS ENDPLUMED OPES_EXPANDED TORSION ECV_MULTITHERMAL PRINT ENERGY | colvar opes generic setup |
22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | WHOLEMOLECULES PRINT TORSION | generic colvar |
22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | CONVERT_TO_FES HISTOGRAM MOLINFO READ METAD DUMPGRID TORSION PUCKERING PRINT | generic colvar bias gridtools |
22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | GROUP MATHEVAL UNITS OPES_METAD COM UPPER_WALLS DISTANCE CUSTOM PYTORCH_MODEL COORDINATION LOAD OPES_METAD_EXPLORE PRINT LOWER_WALLS | core function vatom generic setup colvar opes pytorch bias |
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 | OPT_AVERAGED_SGD UNITS TD_WELLTEMPERED UPPER_WALLS BF_CUBIC_B_SPLINES BF_CHEBYSHEV BF_GAUSSIANS INCLUDE BF_LEGENDRE ENERGY POSITION BF_WAVELETS COORDINATION VES_OUTPUT_BASISFUNCTIONS FLUSH DISTANCE METAD OPT_ADAM TD_UNIFORM PRINT VES_LINEAR_EXPANSION | generic setup colvar ves bias |
21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | ONES GROUP CONTACT_MATRIX VOLUME MATRIX_VECTOR_PRODUCT CENTER METAD INCLUDE LOAD COMBINE MEAN PRINT COORDINATIONNUMBER ENERGY | core symfunc adjmat vatom function generic setup matrixtools colvar bias |
21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | GROUP UNITS PBMETAD COORDINATION WHOLEMOLECULES | core generic setup colvar bias |
21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | UNITS UPPER_WALLS HISTOGRAM CONTACT_MATRIX COMMITTOR DUMPGRID MOVINGRESTRAINT CONVERT_TO_FES LOAD SUM COORDINATIONNUMBER ONES GROUP MORE_THAN FLUSH MATRIX_VECTOR_PRODUCT METAD MEAN PRINT REWEIGHT_METAD | core symfunc adjmat function generic setup matrixtools bias gridtools |
21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | MATHEVAL CONSTANT RESTART TORSION PBMETAD WHOLEMOLECULES PRINT BIASVALUE | function generic setup colvar bias |
20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | GROUP CONVERT_TO_FES DISTANCES HISTOGRAM DUMPGRID READ MOLINFO EMMI RMSD WHOLEMOLECULES PRINT BIASVALUE | core isdb generic multicolvar colvar bias gridtools |
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 | GROUP MATHEVAL COM UPPER_WALLS MOLINFO DISTANCE CONSTANT METAD CONTACTMAP INCLUDE LOAD WHOLEMOLECULES PROJECTION_ON_AXIS PRINT BIASVALUE FUNCPATHGENERAL LOWER_WALLS | core function vatom generic setup colvar bias |
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 | OPT_AVERAGED_SGD TD_WELLTEMPERED DISTANCE_MATRIX UPPER_WALLS CUSTOM BF_LEGENDRE CONTACT_MATRIX ENVIRONMENTSIMILARITY RESTART OPT_DUMMY SUM ONES GROUP MATHEVAL MORE_THAN VOLUME MATRIX_VECTOR_PRODUCT COMBINE Q6 MEAN PRINT SPHERICAL_HARMONIC VES_LINEAR_EXPANSION | core symfunc adjmat function generic setup matrixtools envsim ves colvar bias |
20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | MATHEVAL UPPER_WALLS MOLINFO CENTER METAD DISTANCE RMSD WHOLEMOLECULES COMBINE PRINT LOWER_WALLS ENERGY | function vatom generic colvar bias |
19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | ONES GROUP CONTACT_MATRIX UNITS FLUSH ENDPLUMED MATRIX_VECTOR_PRODUCT METAD RESTART CUSTOM COMBINE MEAN PRINT SUM EXTERNAL COORDINATIONNUMBER | core symfunc adjmat function generic setup matrixtools bias |
19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | GROUP ENDPLUMED DUMPDERIVATIVES DISTANCE CENTER RESTRAINT TORSION CUSTOM COMBINE PRINT ANGLE | core vatom function generic colvar bias |
19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | METAD TORSION INCLUDE RANDOM_EXCHANGES PRINT | colvar generic bias |
19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | UNITS FLUSH UPPER_WALLS DISTANCE METAD COMBINE PRINT ENERGY | function generic setup colvar bias |
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 | UPPER_WALLS COM DISTANCE METAD PRINT ENERGY | colvar generic bias vatom |
19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | UPPER_WALLS FUNCPATHMSD METAD PIV CELL PRINT LOWER_WALLS | function generic colvar piv bias |
19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | UPPER_WALLS COM DISTANCE METAD WHOLEMOLECULES PRINT LOWER_WALLS | colvar generic bias vatom |
19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | GROUP UPPER_WALLS MOLINFO CONSTANT METAD TORSION CUSTOM WHOLEMOLECULES COMBINE GYRATION SUM PRINT ALPHABETA LOWER_WALLS | core function generic multicolvar colvar bias |
19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | CLUSTER_WITHSURFACE CONTACT_MATRIX COMMITTOR FLUSH ENDPLUMED LOCAL_Q6 Q6 DFSCLUSTERING CLUSTER_NATOMS OUTPUT_CLUSTER MFILTER_MORE | clusters symfunc adjmat generic multicolvar |
19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | METAD TORSION WHOLEMOLECULES GYRATION PRINT | colvar generic bias |
19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | ENDPLUMED LESS_THAN MOLINFO METAD WHOLEMOLECULES GYRATION SECONDARY_STRUCTURE_RMSD ALPHARMSD PRINT SUM ENERGY | function generic colvar secondarystructure bias |
19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | MATHEVAL MOLINFO CONSTANT TORSION INCLUDE PUCKERING BIASVALUE | generic colvar function bias |
19.006 | Flying Gaussian proof | methods | flying Gaussians, alanine dipeptide | Vojtech Spiwok | PRINT METAD TORSION | generic colvar bias |
24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | MOLINFO TORSION RESTART PRINT PUCKERING METAD | bias colvar generic setup |
24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | MOLINFO TORSION COORDINATION INCLUDE GROUP BIASVALUE CELL RMSD UPPER_WALLS ENDPLUMED POSITION WHOLEMOLECULES LOAD PRINT CUSTOM UNITS LOWER_WALLS DISTANCE ENERGY MATHEVAL | colvar core function setup bias generic |
24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT CLUSTER_NATOMS CONTACT_MATRIX METAD DFSCLUSTERING UPPER_WALLS SUM UNITS PRINT CLUSTER_PROPERTIES ONES GROUP LESS_THAN MEAN | symfunc core matrixtools adjmat generic setup bias clusters 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 EMMIVOX UPPER_WALLS PRINT INCLUDE DISTANCE WRAPAROUND GROUP BIASVALUE WHOLEMOLECULES | isdb colvar core bias generic |
23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | CENTER FLUSH COM DISTANCES METAD POSITION CUSTOM PRINT UNITS SUM DISTANCE BETWEEN GROUP LESS_THAN WHOLEMOLECULES | colvar core vatom multicolvar function setup bias 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 REWEIGHT_METAD HISTOGRAM RMSD METAD PRINT CONVERT_TO_FES READ MATHEVAL DUMPGRID DISTANCE WHOLEMOLECULES | colvar gridtools function bias generic |
23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | COMBINE TORSION FLUSH COM UPPER_WALLS PRINT DISTANCE METAD WHOLEMOLECULES | colvar vatom generic bias function |
23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | PAIRENTROPY FUNCPATHMSD Q6 RESTRAINT UPPER_WALLS Q4 CUSTOM UNITS PRINT LOCAL_AVERAGE ENERGY PIV VOLUME METAD | colvar symfunc piv gridtools generic setup bias function |
23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | MATRIX_VECTOR_PRODUCT DISTANCE_MATRIX UPPER_WALLS ECV_UMBRELLAS_LINE MORE_THAN RESTART PRINT OPES_EXPANDED LOWER_WALLS CUSTOM INCLUDE SUM GROUP ONES ENVIRONMENTSIMILARITY MEAN | opes core matrixtools adjmat envsim generic setup bias function |
22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | COM UPPER_WALLS ANGLE MOVINGRESTRAINT LOWER_WALLS PRINT DISTANCE METAD WHOLEMOLECULES | bias colvar vatom generic |
22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | CENTER DISTANCES PRINT DISTANCE GROUP METAD MEAN | colvar core vatom multicolvar function bias generic |
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 | COMBINE COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT FLUSH COM COORDINATION CONTACT_MATRIX UPPER_WALLS UNITS LOWER_WALLS CUSTOM DISTANCE GYRATION ONES GROUP METAD MEAN | colvar symfunc core vatom matrixtools adjmat function setup bias generic |
21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | COORDINATIONNUMBER CENTER MATRIX_VECTOR_PRODUCT TORSION COMMITTOR CONTACT_MATRIX ENDPLUMED PRINT DISTANCE ONES GROUP METAD MEAN | colvar symfunc core vatom matrixtools adjmat function bias generic |
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 | COMBINE COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT COORDINATION CONTACT_MATRIX UPPER_WALLS LOWER_WALLS PRINT DISTANCE ONES GROUP METAD MEAN | colvar symfunc core matrixtools adjmat generic bias function |
21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | MOLINFO TORSION DISTANCE_MATRIX INCLUDE ONES ENVIRONMENTSIMILARITY GROUP VOLUME COMBINE RMSD FLUSH ENDPLUMED WHOLEMOLECULES MATRIX_VECTOR_PRODUCT CONTACTMAP LOAD Q6 CONTACT_MATRIX MORE_THAN SUM PRINT UNITS CUSTOM PYTORCH_MODEL DISTANCE ENERGY SPHERICAL_HARMONIC ECV_MULTITHERMAL OPES_METAD OPES_EXPANDED MEAN | colvar opes core symfunc matrixtools adjmat pytorch envsim function setup generic |
21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | LOAD RESTRAINT PRINT DISTANCE GROUP FIXEDATOM | colvar core vatom setup bias generic |
21.021 | ATLAS | methods | Machine Learning, Metadynamics | Federico Giberti | COORDINATIONNUMBER TORSION METAD COORDINATION PRINT UNITS DUMPATOMS MATHEVAL GYRATION GROUP BIASVALUE DISTANCE WHOLEMOLECULES | colvar symfunc core function setup bias generic |
21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | COORDINATIONNUMBER OPT_AVERAGED_SGD MOVINGRESTRAINT CONVERT_TO_FES ONES GROUP BIASVALUE REWEIGHT_METAD COMBINE HISTOGRAM FLUSH BF_CHEBYSHEV UPPER_WALLS VES_LINEAR_EXPANSION MATRIX_VECTOR_PRODUCT LOAD CONTACT_MATRIX RESTRAINT MORE_THAN SUM UNITS PRINT CUSTOM DISTANCE ANN REWEIGHT_BIAS TD_WELLTEMPERED CONSTANT OPES_METAD DUMPGRID METAD MEAN | colvar opes symfunc core matrixtools gridtools adjmat function setup bias annfunc generic ves |
21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | MOLINFO TORSION PBMETAD BIASVALUE COMBINE ANTIBETARMSD SECONDARY_STRUCTURE_RMSD WHOLEMOLECULES CONTACTMAP SAXS STATS SUM CUSTOM PRINT ENSEMBLE LESS_THAN ALPHABETA CENTER CONSTANT GYRATION METAD | colvar isdb secondarystructure vatom multicolvar function bias generic |
20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | COMBINE TORSION LOAD DISTANCES UPPER_WALLS UNITS PRINT LOWER_WALLS DISTANCE ENERGY GROUP | colvar core multicolvar generic setup bias function |
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 | MOLINFO TORSION PBMETAD METAINFERENCE COORDINATION INCLUDE GROUP ALPHARMSD COMBINE FLUSH PARABETARMSD ENDPLUMED ANTIBETARMSD WHOLEMOLECULES STATS PRINT ENSEMBLE CS2BACKBONE DIHCOR GYRATION | isdb colvar core secondarystructure multicolvar function bias generic |
20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | TORSION FLUSH LOAD COM OPES_METAD UPPER_WALLS ENDPLUMED PRINT UNITS LOWER_WALLS PYTORCH_MODEL DISTANCE GROUP MATHEVAL | colvar opes core vatom pytorch function setup bias generic |
19.079 | Impact of Glutamate Carboxylation in the Adsorption of the alpha-1 Domain of Osteocalcin to Hydroxyapatite and Titania | bio | metadynamics, peptide adsorption, parallel tempering, well-tempered ensemble | Sarah Alamdari | MOLINFO COM UPPER_WALLS GYRATION PRINT DISTANCE ENERGY GROUP METAD | colvar core vatom bias generic |
19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | MOLINFO COM UPPER_WALLS PRINT DISTANCE GYRATION ENERGY METAD | bias vatom colvar generic |
19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | LOCAL_Q6 COORDINATIONNUMBER OUTPUT_CLUSTER MATRIX_VECTOR_PRODUCT CLUSTER_NATOMS CONTACT_MATRIX Q6 DFSCLUSTERING METAD DISTANCES MORE_THAN CUSTOM PRINT CLUSTER_PROPERTIES OUTER_PRODUCT ONES SMAC CLUSTER_DISTRIBUTION | symfunc matrixtools multicolvar adjmat generic bias clusters function |
19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | TORSION ENDPLUMED PRINT MATHEVAL METAD | bias colvar generic function |
19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | MOLINFO CENTER SAXS RMSD RESTRAINT UPPER_WALLS STATS ENDPLUMED PRINT INCLUDE DISTANCE GROUP BIASVALUE WHOLEMOLECULES | isdb colvar core vatom function bias generic |
19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | MOLINFO EMMI PRINT GROUP BIASVALUE WHOLEMOLECULES | bias isdb generic core |
24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | LOWEST MATHEVAL SORT DISTANCES UPPER_WALLS DISTANCE WHOLEMOLECULES GROUP COMBINE PRINT POSITION METAD CENTER MOLINFO GHOST | bias function multicolvar generic vatom core colvar |
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 | MATHEVAL ENERGY COORDINATIONNUMBER TORSION FLUSH DISTANCE BIASVALUE PRINT METAD RESTRAINT MOLINFO RESTART COMMITTOR | function generic setup colvar symfunc bias |
24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | TORSION WHOLEMOLECULES PRINT METAD FLUSH RESTART | bias generic setup colvar |
24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | MOVINGRESTRAINT TORSION COM ALPHABETA DISTANCE WHOLEMOLECULES COORDINATION GYRATION PRINT INCLUDE | bias multicolvar generic vatom colvar |
24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | TORSION PRINT METAD RESTART UNITS | bias generic setup 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 | ANGLE WHOLEMOLECULES CENTER COMMITTOR ENERGY GROUP ENDPLUMED MOLINFO OPES_METAD INCLUDE MATHEVAL PYTORCH_MODEL UPPER_WALLS RMSD COMBINE PRINT LOWER_WALLS CONTACTMAP FIXEDATOM CUSTOM FIT_TO_TEMPLATE DISTANCE COORDINATION | bias opes function generic pytorch vatom core colvar |
22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | Q6 MATRIX_VECTOR_PRODUCT LOAD METAD CENTER SUM Q4 GROUP MEAN INCLUDE PAIRENTROPY MATHEVAL CONTACT_MATRIX COMBINE PRINT CUSTOM MORE_THAN COORDINATIONNUMBER ONES SPHERICAL_HARMONIC | gridtools function generic setup vatom matrixtools core adjmat symfunc bias |
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 | TORSION COM DISTANCE WHOLEMOLECULES GROUP PRINT METAD | generic vatom core colvar bias |
22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | WHOLEMOLECULES LOAD GROUP BIASVALUE PRINT MOLINFO EMMIVOX | generic setup isdb core bias |
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 | CENTER DISTANCE PRINT CONTACTMAP | generic colvar vatom |
22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | REWEIGHT_BIAS COM DISTANCES HISTOGRAM DISTANCE GROUP COMBINE CONVERT_TO_FES GYRATION PRINT DUMPGRID METAD MEAN INCLUDE | bias function multicolvar generic vatom colvar core gridtools |
21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | MOVINGRESTRAINT TORSION UPPER_WALLS CONSTANT LOAD COMBINE LOWER_WALLS PRINT METAD ENSEMBLE RESTRAINT CUSTOM UNITS | bias function generic setup colvar |
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 PRINT FIXEDATOM METAD | bias generic vatom colvar |
21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | COM UPPER_WALLS DISTANCE WHOLEMOLECULES PRINT PATHMSD METAD UNITS | generic setup vatom colvar bias |
21.024 | Property map collective variable as a useful tool for force field correction | chemistry | molecular mechanics | Vojtech Spiwok | TORSION PROPERTYMAP WHOLEMOLECULES BIASVALUE PRINT METAD | bias generic colvar |
21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | MATHEVAL PYTORCH_MODEL UPPER_WALLS LOAD GROUP LOWER_WALLS PRINT FLUSH OPES_METAD | opes function generic pytorch setup 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 | UPPER_WALLS WHOLEMOLECULES LOWER_WALLS PATHMSD PRINT METAD RESTART | setup generic colvar bias |
20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | MATHEVAL ENERGY ANGLE PYTORCH_MODEL FIT_TO_TEMPLATE UPPER_WALLS WHOLEMOLECULES DISTANCE GROUP COORDINATION PRINT FIXEDATOM CENTER ENDPLUMED OPES_METAD | opes function generic pytorch vatom colvar core bias |
20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | Q6 ECV_MULTITHERMAL MATRIX_VECTOR_PRODUCT WHOLEMOLECULES LOAD VOLUME ECV_LINEAR DISTANCE_MATRIX SUM ENERGY GROUP ENVIRONMENTSIMILARITY ENDPLUMED MOLINFO MEAN ECV_MULTITHERMAL_MULTIBARIC MATHEVAL TORSION CONTACT_MATRIX UPPER_WALLS RMSD COMBINE PRINT OPES_EXPANDED CUSTOM UNITS MORE_THAN ECV_UMBRELLAS_LINE ONES SPHERICAL_HARMONIC POSITION | bias opes function generic setup envsim matrixtools core adjmat symfunc colvar |
20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | DISTANCES WHOLEMOLECULES DISTANCE COORDINATION GROUP PRINT CENTER CUSTOM SUM RESTART | function multicolvar generic setup vatom core colvar |
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 | MATRIX_VECTOR_PRODUCT METAD CENTER SUM ENERGY GROUP GYRATION ENDPLUMED MEAN LOWEST DISTANCES CONTACT_MATRIX UPPER_WALLS LOWER_WALLS PRINT MORE_THAN COORDINATIONNUMBER ONES DISTANCE | bias function multicolvar generic vatom matrixtools core adjmat symfunc colvar |
19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | TORSION PRINT POSITION METAD ENDPLUMED OPES_METAD EXTERNAL UNITS | opes generic setup colvar bias |
19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_OPTIMIZER_BIAS MAZE_SIMULATED_ANNEALING PRINT POSITION MAZE_LOSS UNITS | setup generic colvar maze |
19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | COM COMBINE ANN POSITION RESTRAINT | function annfunc vatom colvar bias |
19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_OPTIMIZER_BIAS MAZE_SIMULATED_ANNEALING PRINT POSITION MAZE_LOSS UNITS | setup generic colvar maze |
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 | TORSION FUNNEL COM DISTANCES REWEIGHT_METAD UPPER_WALLS ALPHABETA WHOLEMOLECULES RMSD GROUP DISTANCE COMBINE LOWER_WALLS PRINT BRIDGE METAD MOLINFO | function multicolvar generic vatom funnel colvar core adjmat bias |
19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | COM FUNNEL UPPER_WALLS DISTANCE WHOLEMOLECULES RMSD FUNNEL_PS LOWER_WALLS PRINT METAD | generic funnel vatom colvar bias |
19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | LOWEST COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT DISTANCES CONTACT_MATRIX CENTER ONES DISTANCE GROUP GYRATION PRINT METAD ENDPLUMED SUM RESTART MEAN MORE_THAN | bias function multicolvar generic setup vatom matrixtools core adjmat symfunc colvar |
19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | CS2BACKBONE METAINFERENCE WHOLEMOLECULES GROUP RDC PRINT MOLINFO | isdb core generic |
24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | GROUP RESTRAINT PRINT MOLINFO EMMIVOX BIASVALUE ERMSD INCLUDE WHOLEMOLECULES | generic bias isdb core colvar |
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 | WHOLEMOLECULES PRINT DRR FLUSH MOLINFO METAD RMSD LOWER_WALLS UPPER_WALLS COORDINATION PYTORCH_MODEL | drr generic bias pytorch colvar |
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 | PRINT FLUSH MATHEVAL SUM INCLUDE SELECT_COMPONENTS TRANSPOSE METAD | matrixtools generic bias function valtools |
23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | SECONDARY_STRUCTURE_RMSD LESS_THAN PRINT MOLINFO FIT_TO_TEMPLATE COMBINE POSITION SUM ANN METAD ALPHARMSD WHOLEMOLECULES | secondarystructure generic bias annfunc function colvar |
23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | ENDPLUMED UNITS PRINT CUSTOM POSITION OPES_METAD BIASVALUE LOWER_WALLS UPPER_WALLS PYTORCH_MODEL | generic bias pytorch setup function colvar opes |
23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | PRINT CONSTANT MATHEVAL BIASVALUE PBMETAD DISTANCE ANGLE WHOLEMOLECULES | function colvar generic bias |
23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | GROUP PRINT CUSTOM COM OPES_METAD_EXPLORE CENTER METAD DISTANCE LOWER_WALLS UPPER_WALLS COORDINATION WHOLEMOLECULES | colvar generic bias core function vatom opes |
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 | PRINT CONSTANT MATHEVAL BIASVALUE METAD DISTANCE LOWER_WALLS UPPER_WALLS WHOLEMOLECULES | function colvar generic bias |
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 | HISTOGRAM GROUP PRINT DISTANCE_MATRIX CUSTOM DUMPGRID SUM LOWER_WALLS OPES_EXPANDED RESTART ENVIRONMENTSIMILARITY MORE_THAN ECV_UMBRELLAS_LINE MATRIX_VECTOR_PRODUCT ONES UPPER_WALLS | gridtools envsim matrixtools generic bias core adjmat setup function opes |
22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | CUSTOM MOLINFO POSITION OPES_METAD CONTACTMAP PYTORCH_MODEL ENDPLUMED TORSION INCLUDE COMMITTOR UNITS PRINT CONSTANT COMBINE BIASVALUE RMSD GROUP ENERGY DISTANCE WHOLEMOLECULES | generic bias core pytorch setup function colvar opes |
22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | WHOLEMOLECULES PRINT PATHMSD COM METAD FUNNEL DISTANCE LOWER_WALLS UPPER_WALLS FUNNEL_PS | colvar generic bias funnel vatom |
22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | PRINT TORSION BF_FOURIER VES_LINEAR_EXPANSION TD_UNIFORM OPT_AVERAGED_SGD | ves colvar generic |
22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | ENDPLUMED ECV_MULTITHERMAL ECV_UMBRELLAS_FILE UNITS PRINT CUSTOM TORSION ENERGY OPES_METAD_EXPLORE POSITION OPES_METAD OPES_EXPANDED BIASVALUE METAD LOWER_WALLS UPPER_WALLS PBMETAD | generic bias setup function colvar opes |
21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | CENTER PRINT DISTANCE | vatom generic colvar |
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 | LOWEST SECONDARY_STRUCTURE_RMSD MOLINFO METAD ALPHARMSD UPPER_WALLS DIHEDRAL_CORRELATION DIHCOR SUM ANTIBETARMSD LOWER_WALLS LESS_THAN PRINT PARABETARMSD RANDOM_EXCHANGES COORDINATION GROUP ENERGY GYRATION WHOLEMOLECULES | secondarystructure generic bias multicolvar core function colvar |
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 | ENDPLUMED PRINT TORSION RANDOM_EXCHANGES INCLUDE METAD PBMETAD | colvar generic bias |
21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | RESTRAINT UNITS PRINT CUSTOM TORSION CONSTANT COMBINE LOAD INCLUDE CENTER METAD DISTANCE MOVINGRESTRAINT UPPER_WALLS WHOLEMOLECULES | generic bias vatom setup function colvar |
21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | SECONDARY_STRUCTURE_RMSD LESS_THAN PRINT MOLINFO MATHEVAL ENERGY SUM INCLUDE CONTACTMAP METAD DISTANCE LOWER_WALLS ALPHARMSD UPPER_WALLS WHOLEMOLECULES | secondarystructure generic bias function colvar |
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 | |
21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | GROUP PRINT COM DISTANCE WHOLEMOLECULES | vatom core generic colvar |
20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | WHOLEMOLECULES PRINT CENTER COORDINATION PBMETAD | vatom generic bias colvar |
20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | GROUP PRINT LOAD INCLUDE CENTER METAD UPPER_WALLS VOLUME | colvar generic bias core setup vatom |
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 | GROUP UNITS PRINT CUSTOM SUM DISTANCES CENTER METAD DISTANCE COORDINATION | colvar generic bias multicolvar core setup function vatom |
19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | PRINT TORSION MOLINFO FLUSH MATHEVAL COM SORT INCLUDE METAD DISTANCE MAXENT COORDINATION WHOLEMOLECULES | colvar generic bias function vatom |
19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | HISTOGRAM PRINT TORSION EXTERNAL REWEIGHT_BIAS DUMPGRID MATHEVAL READ REWEIGHT_METAD BIASVALUE METAD DISTANCE CONVERT_TO_FES COMMITTOR | gridtools generic bias function colvar |
19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | UNITS PRINT PATHMSD RESTART METAD LOWER_WALLS UPPER_WALLS | colvar generic bias setup |
19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | UNITS PRINT FLUSH COMBINE ENERGY METAD DISTANCE LOWER_WALLS UPPER_WALLS | generic bias setup function colvar |
19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | GROUP MATRIX_VECTOR_PRODUCT ENDPLUMED UNITS FCCUBIC_FUNC CUSTOM MEAN PRINT SUM FCCUBIC CONTACT_MATRIX METAD MORE_THAN CELL ONES UPPER_WALLS | matrixtools generic bias symfunc core adjmat setup function colvar |
19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | UNITS PRINT FLUSH COMBINE DISTANCES RESTART METAD DISTANCE UPPER_WALLS | generic bias multicolvar setup function colvar |
19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | STATS CUSTOM MOLINFO UPPER_WALLS PBMETAD DIHEDRAL_CORRELATION ENDPLUMED DIHCOR TORSION ALPHABETA SUM DHENERGY PRINT CONSTANT COMBINE METAINFERENCE GROUP RESTRAINT CENTER DISTANCE RDC ENSEMBLE WHOLEMOLECULES | generic bias isdb multicolvar core vatom function colvar |
19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | GROUP PRINT ALPHABETA MOLINFO INCLUDE METAINFERENCE PBMETAD CENTER DISTANCE GYRATION COORDINATION CS2BACKBONE WHOLEMOLECULES | colvar generic bias isdb core multicolvar vatom |
24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | COORDINATION DISTANCE GYRATION PBMETAD TORSION ANTIBETARMSD PRINT ALPHARMSD INCLUDE PARABETARMSD MOLINFO DIHCOR WHOLEMOLECULES FLUSH COMBINE ENDPLUMED GROUP | generic core multicolvar secondarystructure bias function colvar |
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 | DISTANCE PRINT | generic colvar |
24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | UNITS METAD TORSION PRINT GROUP | generic core setup bias colvar |
24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | UNITS DISTANCE PRINT CUSTOM BIASVALUE | generic setup bias function colvar |
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 | UNITS DISTANCE TORSION PRINT OPES_METAD CUSTOM UPPER_WALLS COMMITTOR FLUSH COMBINE LOWER_WALLS | generic setup bias function opes colvar |
23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | UNITS DISTANCE PRINT WHOLEMOLECULES COMBINE METAD | generic setup bias function colvar |
23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | CENTER DISTANCE RESTRAINT DUMPMASSCHARGE PRINT FIXEDATOM MOLINFO UPPER_WALLS COMBINE METAD | generic vatom function bias colvar |
23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | CENTER MORE_THAN METAD COORDINATIONNUMBER MEAN ONES PRINT SUM INCLUDE LOAD CUSTOM MATRIX_VECTOR_PRODUCT CONTACT_MATRIX GROUP | generic core setup vatom function bias adjmat symfunc matrixtools |
23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | DISTANCE ZDISTANCES DISTANCES OPES_METAD CUSTOM CENTER MEAN ENERGY LESS_THAN UPPER_WALLS COMMITTOR CONTACT_MATRIX FLUSH LOWER_WALLS ONES SUM FIXEDATOM MATRIX_VECTOR_PRODUCT GROUP UNITS COORDINATIONNUMBER PRINT MATHEVAL COM | generic core multicolvar setup vatom function bias opes colvar adjmat symfunc matrixtools |
23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | DISTANCE DISTANCES WHOLEMOLECULES RESTART METAD CENTER WRAPAROUND POSITION UPPER_WALLS FLUSH LOWER_WALLS LOWEST DUMPATOMS GROUP UNITS FIT_TO_TEMPLATE PRINT MATHEVAL COM | generic core multicolvar setup bias vatom function colvar |
23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | COORDINATION DISTANCE GYRATION PRINT COM UPPER_WALLS PBMETAD | generic bias colvar vatom |
23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | ANGLE SECONDARY_STRUCTURE_RMSD DISTANCE CONTACTMAP DUMPFORCES PRINT LESS_THAN SUM ALPHARMSD COM MOLINFO METAD | generic secondarystructure vatom function bias colvar |
22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | UNITS DISTANCE PRINT COM CUSTOM DRR FLUSH METAD BIASVALUE | generic setup vatom function bias colvar drr |
22.014 | Quasi Liquid Layer Order Parameters | materials | Quasi-Liquid Layer, Steinhardt Order Parameter, Entropy Fingerprint | Jihong Shi | HISTOGRAM UNITS Q3 PAIRENTROPIES Q6 LOCAL_Q3 LOCAL_Q6 LOAD LOCAL_Q4 DUMPMULTICOLVAR Q4 ENDPLUMED LOCAL_AVERAGE DUMPGRID | generic multicolvar setup gridtools symfunc |
22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | CENTER COORDINATION ANGLE DISTANCE FIT_TO_TEMPLATE ENERGY PRINT FIXEDATOM MATHEVAL PYTORCH_MODEL LOAD UPPER_WALLS COMMITTOR WHOLEMOLECULES FLUSH ENDPLUMED GROUP | generic core setup vatom function bias colvar pytorch |
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 | GYRATION METAD TORSION PRINT ALPHABETA SUM CUSTOM UPPER_WALLS CONSTANT WHOLEMOLECULES COMBINE LOWER_WALLS ENDPLUMED GROUP | generic core multicolvar bias function colvar |
21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | DISTANCE TORSIONS PRINT KDE MATHEVAL COM | generic multicolvar gridtools vatom function colvar |
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 | CENTER COORDINATION RESTRAINT REWEIGHT_BIAS PRINT MATHEVAL POSITION WHOLEMOLECULES RESTART METAD | generic setup vatom function bias colvar |
21.007 | Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling | bio | metadynamics, machine learning, protein folding | Vojtech Spiwok | SECONDARY_STRUCTURE_RMSD FIT_TO_TEMPLATE LESS_THAN MATHEVAL ALPHARMSD SUM POSITION MOLINFO WHOLEMOLECULES COMBINE | function secondarystructure generic colvar |
20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | DISTANCE RMSD TORSION PRINT MOLINFO UPPER_WALLS WHOLEMOLECULES COMBINE RESTART METAD | generic setup bias function colvar |
19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | COORDINATION DISTANCE RESTRAINT WHOLEMOLECULES ENDPLUMED LOWER_WALLS | bias generic colvar |
19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | DISTANCE ERMSD RMSD TORSION PRINT MOLINFO WHOLEMOLECULES METAD | generic colvar bias |
19.055 | Flying Gaussian method | methods | flying Gaussians, alanine dipeptide, peptide bond, Met-enkephalin | Vojtech Spiwok | DISTANCE TORSION PRINT MATHEVAL COMBINE METAD | generic function colvar bias |
19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | CELL CUSTOM METAD AROUND MEAN LESS_THAN FCCUBIC UPPER_WALLS CONTACT_MATRIX FCCUBIC_FUNC ENDPLUMED LOWER_WALLS ONES SUM MATRIX_VECTOR_PRODUCT GROUP MORE_THAN UNITS PRINT | generic core volumes setup bias function colvar adjmat symfunc matrixtools |
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 RESTRAINT TORSION PRINT COM GROUP | generic core bias vatom colvar |
19.027 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, liquid sodium, density anomaly | Pablo Piaggi | HISTOGRAM AVERAGE REWEIGHT_BIAS CONVERT_TO_FES CUSTOM COMBINE RESTART TD_MULTICANONICAL ACCUMULATE ENERGY DUMPGRID VES_LINEAR_EXPANSION BF_LEGENDRE OPT_DUMMY UNITS OPT_AVERAGED_SGD READ PRINT REWEIGHT_TEMP_PRESS | generic setup gridtools bias function colvar ves |
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 | DISTANCE RESTART PATH SUM FIXEDATOM GROUP COMBINE EUCLIDEAN_DISTANCE COORDINATION WHOLEMOLECULES LOWEST OPES_METAD CONSTANT CUSTOM TORSION UPPER_WALLS PYTORCH_MODEL CENTER PDB2CONSTANT LOWER_WALLS FIT_TO_TEMPLATE | bias opes colvar mapping pytorch setup vatom generic core refdist function |
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 | LOAD TORSION METAD COMMITTOR GROUP PRINT | bias colvar setup generic core |
24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | DISTANCE COMBINE MOLINFO BIASVALUE LOWER_WALLS GHBFIX UPPER_WALLS COORDINATION DEBUG METAD COM GROUP CENTER PRINT | bias colvar generic vatom core function |
24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | DISTANCE CONTACTMAP PATH HISTOGRAM FIXEDATOM COMMITTOR GROUP COMBINE MOLINFO MATHEVAL COORDINATION WHOLEMOLECULES GPATH REWEIGHT_METAD FLUSH METAD INCLUDE PRINT DUMPGRID UPPER_WALLS RMSD COM READ CONVERT_TO_FES WRAPAROUND ENDPLUMED FIT_TO_TEMPLATE | bias colvar mapping vatom generic gridtools core function |
23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | DISTANCE GYRATION MOLINFO UPPER_WALLS PBMETAD COM LOWER_WALLS PRINT | generic vatom colvar bias |
23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | DISTANCE DISSIMILARITIES TRANSPOSE SUM PROJECT_POINTS EUCLIDEAN_DISTANCE VORONOI WHOLEMOLECULES METAD CONSTANT LANDMARK_SELECT_FPS PRINT CUSTOM MORE_THAN VSTACK UPPER_WALLS SKETCHMAP COM PATHMSD SKETCHMAP_PROJECTION PDB2CONSTANT COLLECT_FRAMES | bias colvar matrixtools landmarks generic vatom valtools dimred refdist function |
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 | READ TORSION EXTRACV PUT METAD PRINT | generic colvar core bias |
22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | METAD PRINT TORSION | bias colvar generic |
22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | UPPER_WALLS PCAVARS WHOLEMOLECULES METAD LOWER_WALLS PRINT | bias mapping 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 CUSTOM COMBINE MOLINFO TORSION ALPHARMSD UPPER_WALLS SECONDARY_STRUCTURE_RMSD LESS_THAN WHOLEMOLECULES COORDINATION SUM METAD PRINT FLUSH ALPHABETA CONSTANT ANGLE | bias colvar multicolvar generic secondarystructure function |
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 CUSTOM COMBINE COORDINATION METAD VOLUME PRINT | generic colvar bias function |
21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | DISTANCE BF_CHEBYSHEV HISTOGRAM EXTERNAL RESTRAINT GROUP COMBINE LOAD UWALLS MATRIX_VECTOR_PRODUCT DISTANCES COORDINATION REWEIGHT_METAD FLUSH METAD OPT_AVERAGED_SGD PRINT COORD_ANGLES UNITS CUSTOM VES_LINEAR_EXPANSION DUMPGRID UPPER_WALLS MEAN TD_GRID REWEIGHT_BIAS COORDINATIONNUMBER CONTACT_MATRIX ONES CONVERT_TO_FES ANGLES LOWER_WALLS | bias colvar symfunc ves setup matrixtools adjmat generic gridtools multicolvar core function |
21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | AROUND DFSCLUSTERING LOAD DUMPGRID DENSITY COORDINATIONNUMBER CONTACT_MATRIX CLUSTER_DISTRIBUTION CLUSTER_NATOMS MULTICOLVARDENS FIXEDATOM MFILTER_MORE RESTRAINT GROUP PRINT | bias symfunc setup adjmat vatom clusters volumes gridtools generic multicolvar core |
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 | METAD DISTANCE PRINT TORSION | bias 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 | UNITS GYRATION MOVINGRESTRAINT ENDPLUMED PRINT | bias setup colvar generic |
19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | DISTANCE ENDPLUMED INCLUDE GROUP CENTER PRINT | generic vatom colvar core |
19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | UPPER_WALLS WHOLEMOLECULES METAD PATHMSD LOWER_WALLS PRINT | bias colvar generic |
19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | DISTANCE ENDPLUMED CONTACTMAP FUNCPATHMSD WHOLEMOLECULES RMSD METAD COM PRINT | bias colvar generic 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 UPPER_WALLS DISTANCES FLUSH METAD PRINT | bias mapping setup generic multicolvar |
19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | DISTANCE CUSTOM COMBINE COMMITTOR TORSION RESTART WHOLEMOLECULES SUM EXTERNAL ALPHABETA COM CONSTANT PRINT | bias colvar setup generic vatom multicolvar function |
19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | DISTANCE COMBINE TORSION EDS RESTRAINT PRINT | bias colvar generic eds function |
19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | BIASVALUE TORSION MATHEVAL WHOLEMOLECULES METAD CONSTANT PRINT | bias colvar generic function |
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 | WHOLEMOLECULES METAD MOLINFO PRINT DISTANCE RMSD MATHEVAL | bias function generic colvar |
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 | GHBFIX ERMSD COMBINE WHOLEMOLECULES METAD MOLINFO PRINT BIASVALUE COORDINATION | bias function generic colvar |
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 | COMBINE PATH WHOLEMOLECULES UPPER_WALLS CENTER COORDINATION GROUP PRINT DISTANCE FIT_TO_TEMPLATE LOWER_WALLS SUM OPES_METAD_EXPLORE FIXEDATOM EUCLIDEAN_DISTANCE CUSTOM LOWEST CONSTANT OPES_METAD PDB2CONSTANT UNITS TORSION PYTORCH_MODEL | pytorch refdist opes colvar vatom mapping function core bias setup generic |
23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | COM INCLUDE WHOLEMOLECULES PBMETAD RESTRAINT PRINT TORSION GYRATION COORDINATION | bias generic colvar vatom |
22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | PRINT UNITS OPES_METAD_EXPLORE PYTORCH_MODEL CUSTOM COORDINATION | pytorch opes colvar function 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 | CONSTANT METAD COMMITTOR UPPER_WALLS PRINT DISTANCE SUM DRMSD MATHEVAL CELL LOWER_WALLS CUSTOM | bias function generic colvar |
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 | PATHMSD METAD FLUSH PRINT BIASVALUE DRR CUSTOM | colvar drr function bias generic |
22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | COM MOLINFO UPPER_WALLS PBMETAD PRINT DISTANCE GYRATION | bias generic colvar vatom |
22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | COMMITTOR UPPER_WALLS MATRIX_VECTOR_PRODUCT REWEIGHT_BIAS MEAN GROUP ONES PRINT MOVINGRESTRAINT LOAD COORDINATIONNUMBER FLUSH SUM ANN CUSTOM RESTRAINT HISTOGRAM VOLUME CONTACT_MATRIX LESS_THAN UNITS BIASVALUE DUMPGRID CONVERT_TO_FES | symfunc gridtools adjmat colvar function core matrixtools annfunc bias setup generic |
22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | CONSTANT COM ALPHABETA RESTART COMBINE WHOLEMOLECULES ANTIBETARMSD MOLINFO LESS_THAN PBMETAD PRINT SUM TORSION SECONDARY_STRUCTURE_RMSD ALPHARMSD CUSTOM | colvar vatom multicolvar function bias setup generic secondarystructure |
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 |
22.016 | 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 | MORE_THAN DUMPGRID RESTART GROUP VOLUME OPES_METAD HISTOGRAM ONES UPPER_WALLS ENVIRONMENTSIMILARITY PRINT SUM MATRIX_VECTOR_PRODUCT AROUND DISTANCE_MATRIX ENERGY MEAN CUSTOM | envsim gridtools adjmat volumes opes colvar function core matrixtools bias setup generic |
22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | COM COMBINE GROUP CONTACT_MATRIX WHOLEMOLECULES METAD MOLINFO COMMITTOR COORDINATIONNUMBER ONES PRINT DISTANCE SUM MATRIX_VECTOR_PRODUCT RMSD MEAN CUSTOM | symfunc adjmat colvar vatom function core matrixtools bias generic |
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 | METAD WHOLEMOLECULES PRINT LOAD | bias setup generic |
21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | OPT_AVERAGED_SGD VES_LINEAR_EXPANSION RESTART COMBINE VOLUME METAD ENERGY PRINT BF_LEGENDRE TD_WELLTEMPERED PAIRENTROPY LOAD | gridtools colvar function ves bias setup generic |
21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | COM WHOLEMOLECULES METAD UPPER_WALLS PRINT DISTANCE UNITS LOWER_WALLS | colvar vatom bias setup 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 | CONSTANT COM ALPHABETA INCLUDE COMBINE METAD PBMETAD PRINT DISTANCE SUM TORSION GYRATION ENERGY CUSTOM COORDINATION | colvar vatom multicolvar function bias generic |
21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | DISTANCE LOWER_WALLS UPPER_WALLS PRINT | bias generic colvar |
21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | COM METAD UPPER_WALLS PRINT FUNNEL_PS DISTANCE LOWER_WALLS FUNNEL | colvar funnel vatom bias generic |
20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | TORSION ENDPLUMED PRINT | generic colvar |
20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | CONSTANT ALPHABETA ENSEMBLE COMBINE WHOLEMOLECULES MOLINFO PBMETAD FLUSH PRINT DISTANCE CENTER SUM TORSION SAXS GYRATION METAINFERENCE STATS CUSTOM | colvar vatom multicolvar function isdb bias generic |
19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | FCCUBIC_FUNC CHARGE FOURIER_TRANSFORM ARGS2VATOM MULTICOLVARDENS CENTER MATRIX_VECTOR_PRODUCT MORE_THAN FIND_CONTOUR_SURFACE GROUP FCCUBIC ONES ACCUMULATE DISTANCES KDE SUM MASS CUSTOM CONTACT_MATRIX UNITS POSITION DUMPGRID | fourier symfunc gridtools adjmat contour colvar vatom multicolvar function matrixtools core setup generic |
19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | RESTART METAD UPPER_WALLS FLUSH PRINT DISTANCE UNITS MATHEVAL | colvar function bias setup generic |
19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | CS2BACKBONE RDC ENSEMBLE JCOUPLING WHOLEMOLECULES MOLINFO PBMETAD FLUSH PRINT METAINFERENCE TORSION GYRATION BIASVALUE ENDPLUMED STATS | colvar function isdb bias generic |
19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | TORSION DRR PRINT | drr generic colvar |
19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | COMBINE VOLUME METAD UPPER_WALLS PRINT TORSION MATHEVAL ENDPLUMED ENERGY CELL LOWER_WALLS | bias function generic colvar |
19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | METAD COMMITTOR UPPER_WALLS PRINT DISTANCE CENTER TORSION LOWER_WALLS | bias generic colvar vatom |
19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | ERMSD METAD WHOLEMOLECULES MOLINFO PRINT RMSD ENDPLUMED | bias generic colvar |
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 | PRINT DISTANCE UPPER_WALLS ENERGY COORDINATION OPES_METAD | generic bias opes colvar |
23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | GROUP Q4 VOLUME PRINT CONTACT_MATRIX Q6 MEAN MATHEVAL SUM MATRIX_VECTOR_PRODUCT ONES CUSTOM MORE_THAN METAD ENERGY COORDINATIONNUMBER SPHERICAL_HARMONIC COMBINE | core generic function colvar adjmat symfunc bias matrixtools |
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 | GROUP PRINT WRAPAROUND CENTER POSITION MOLINFO WHOLEMOLECULES FIT_TO_TEMPLATE DISTANCE SUM CUSTOM METAD UPPER_WALLS SHADOW DISTANCES | core multicolvar generic function colvar isdb bias vatom |
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 | GROUP PRINT WRAPAROUND CENTER MOLINFO STATS UPPER_WALLS BIASVALUE SAXS DISTANCE ENSEMBLE RMSD | core generic function colvar isdb bias vatom |
23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | PRINT GYRATION DISTANCE COM PBMETAD UPPER_WALLS | generic bias vatom colvar |
22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | GROUP Q4 MFILTER_LESS LOCAL_AVERAGE LOCAL_Q6 DFSCLUSTERING CLUSTER_NATOMS PRINT LOCAL_Q4 Q6 CONTACT_MATRIX MFILTER_MORE COORDINATIONNUMBER COMBINE | core generic function adjmat symfunc clusters multicolvar |
22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | GROUP PRINT MOLINFO GHBFIX BIASVALUE CUSTOM METAD UPPER_WALLS COORDINATION LOAD FLUSH COMBINE | core generic function colvar bias setup |
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 | PRINT RMSD | generic colvar |
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 | DISTANCE_MATRIX GROUP PRINT INCLUDE ENVIRONMENTSIMILARITY LOWER_WALLS MEAN SUM MATRIX_VECTOR_PRODUCT ONES CUSTOM MORE_THAN UPPER_WALLS ECV_UMBRELLAS_LINE OPES_EXPANDED | core generic function adjmat bias envsim matrixtools opes |
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 | LOWER_WALLS MEAN SUM COM DISTANCE XANGLES CONSTANT ALPHABETA YANGLES MOLINFO ZANGLES TORSION CUSTOM COMBINE PRINT WHOLEMOLECULES MATHEVAL METAD UPPER_WALLS | generic function colvar bias vatom multicolvar |
22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | PRINT INCLUDE CENTER RANDOM_EXCHANGES CONTACTMAP ANTIBETARMSD MOLINFO SUM UNITS METAD DISTANCE LESS_THAN COORDINATION ALPHARMSD SECONDARY_STRUCTURE_RMSD | generic secondarystructure function colvar setup bias vatom |
21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | PRINT ERMSD MOLINFO WHOLEMOLECULES BIASVALUE METAD COORDINATION COMBINE | generic bias function colvar |
21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | LOCAL_Q6 CLUSTER_NATOMS INSPHERE MEAN SUM ONES DFSCLUSTERING MATRIX_VECTOR_PRODUCT HISTOGRAM CLUSTER_DISTRIBUTION CONTACT_MATRIX Q6 CUSTOM DUMPGRID COMBINE GROUP PRINT MFILTER_MORE MORE_THAN FIXEDATOM METAD COORDINATIONNUMBER | core gridtools volumes generic function adjmat symfunc bias vatom matrixtools clusters multicolvar |
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 | GROUP PRINT MOLINFO WHOLEMOLECULES RESTART COM UPPER_WALLS BIASVALUE DISTANCE EMMI | core generic colvar isdb bias setup vatom |
21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | LOWER_WALLS DISTANCE OPES_METAD DISTANCES PYTORCH_MODEL CENTER COORDINATION LOAD TORSION UNITS ENDPLUMED GROUP PRINT ANGLE FIT_TO_TEMPLATE WHOLEMOLECULES MATHEVAL FIXEDATOM UPPER_WALLS | opes core generic function colvar bias setup vatom pytorch multicolvar |
21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | PRINT LOWER_WALLS MOLINFO GYRATION COM UPPER_WALLS PBMETAD DISTANCE ENERGY | generic bias vatom colvar |
21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | PRINT TORSION ECV_MULTITHERMAL OPES_EXPANDED ECV_UMBRELLAS_LINE ENERGY OPES_METAD ENDPLUMED | generic opes colvar |
21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | GROUP PRINT REWEIGHT_METAD INCLUDE LOWER_WALLS RANDOM_EXCHANGES MOLINFO WHOLEMOLECULES DISTANCE HISTOGRAM DUMPGRID METAD UPPER_WALLS ENERGY COORDINATION PUCKERING | core gridtools generic colvar bias |
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 | PRINT CENTER ERMSD MOLINFO TORSION ABMD RESTART DISTANCE | generic colvar setup bias vatom |
20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | METAD PRINT TORSION | generic bias colvar |
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 | PRINT RESTRAINT MOLINFO STATS WHOLEMOLECULES COORDINATION | generic bias function colvar |
20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | GROUP PRINT RESTRAINT FISST GYRATION MATHEVAL BIASVALUE UNITS DISTANCE ENERGY | core generic fisst function colvar bias setup |
20.003 | Enhanced sampling of transition states | methods | Variationally Enhanced Sampling, Target distribution, Transition state, Enhanced Sampling, Nucleation, chemical reaction | Jayashrita Debnath | BF_LEGENDRE PRINT POSITION VES_LINEAR_EXPANSION UNITS ENERGY LOAD OPT_AVERAGED_SGD | generic setup ves colvar |
19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | GROUP PRINT CENTER LOWER_WALLS RESTART COM UPPER_WALLS METAD DISTANCE | core generic colvar setup bias vatom |
19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | GROUP PRINT ENSEMBLE INCLUDE CENTER ANGLE MOLINFO WHOLEMOLECULES MATHEVAL STATS BIASVALUE PBMETAD SAXS COORDINATION ALPHABETA ENDPLUMED COMBINE | core multicolvar generic function colvar isdb bias vatom |
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 | GROUP PRINT LOWER_WALLS POSITION RESTART UNITS METAD UPPER_WALLS COORDINATION FLUSH | core generic colvar setup bias |
19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | LOWER_WALLS RESTART SUM LESS_THAN ANTIBETARMSD CONSTANT ALPHABETA SECONDARY_STRUCTURE_RMSD MOLINFO TORSION CUSTOM PBMETAD CS2BACKBONE COMBINE GROUP FLUSH PRINT ENDPLUMED WHOLEMOLECULES BIASVALUE UPPER_WALLS | core generic secondarystructure function colvar isdb setup bias multicolvar |
19.008 | anncolvar | methods | neural network, dimensionality reduction | Vojtech Spiwok | PRINT POSITION MOLINFO FIT_TO_TEMPLATE MATHEVAL WHOLEMOLECULES SUM LESS_THAN METAD ALPHARMSD SECONDARY_STRUCTURE_RMSD COMBINE | generic secondarystructure function colvar bias |
24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | FIXEDATOM COMBINE CONTACTMAP BIASVALUE LOWER_WALLS ENDPLUMED CENTER POSITION GROUP INCLUDE WHOLEMOLECULES PRINT OPES_METAD_EXPLORE OPES_METAD UNITS PYTORCH_MODEL CUSTOM FIT_TO_TEMPLATE METAD MATHEVAL DISTANCE COORDINATION RMSD FLUSH ENERGY UPPER_WALLS MOLINFO | opes colvar function bias pytorch vatom core setup 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 GROUP COORDINATION ANGLE WHOLEMOLECULES TORSION PRINT FIT_TO_TEMPLATE DISTANCE ECV_MULTITHERMAL UPPER_WALLS LOWER_WALLS OPES_METAD_EXPLORE MATHEVAL CENTER ENERGY ENDPLUMED OPES_EXPANDED | opes colvar function bias vatom core generic |
24.015 | nanocluster QM/MM | chemistry | nanocluster, QM/MM, pathCV, OPES, reaction modelling | Vikas Tiwari | PRINT LOWER_WALLS CENTER COMMITTOR FLUSH UPPER_WALLS OPES_METAD DISTANCE RESTRAINT UNITS | opes colvar bias vatom setup generic |
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 PRINT CENTER CONSTANT METAD UPPER_WALLS LOWER_WALLS BIASVALUE MATHEVAL DISTANCE | colvar function bias vatom 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 | COMMITTOR BIASVALUE ENDPLUMED LOWER_WALLS CENTER POSITION GROUP COM WHOLEMOLECULES PRINT OPES_METAD_EXPLORE OPES_METAD WRAPAROUND UNITS CUSTOM TORSION FIT_TO_TEMPLATE MATHEVAL DISTANCE COORDINATION FLUSH ENERGY UPPER_WALLS MOLINFO | opes colvar function bias vatom core setup generic |
23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | COORDINATIONNUMBER GROUP MFILTER_MORE PRINT COMBINE METAD LOWER_WALLS LOCAL_Q6 Q6 MOVINGRESTRAINT | symfunc function bias multicolvar core generic |
23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | CUSTOM FIXEDATOM TORSION PRINT CENTER METAD UPPER_WALLS MATHEVAL DISTANCE | colvar function bias vatom generic |
23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | PATHMSD CUSTOM DRR PRINT METAD BIASVALUE LOWER_WALLS UPPER_WALLS FLUSH | colvar function bias generic drr |
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 | WHOLEMOLECULES PRINT CONTACTMAP METAD ENERGY LOWER_WALLS UPPER_WALLS | generic colvar bias |
22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | DISTANCES ANGLE COMBINE BRIDGE LOWER_WALLS CENTER BRIDGE_MATRIX GROUP WHOLEMOLECULES PRINT UNITS MEAN FIT_TO_TEMPLATE SUM METAD MATHEVAL DISTANCE COORDINATION RMSD UPPER_WALLS FLUSH | adjmat colvar function generic bias vatom core setup multicolvar |
21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | DISTANCE PRINT RMSD | generic colvar |
21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | CUSTOM INCLUDE TORSION PRINT CONSTANT METAD REWEIGHT_METAD BIASVALUE ENERGY DISTANCE UNITS | colvar function bias setup generic |
21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | CUSTOM GROUP INCLUDE ERMSD SAXS WHOLEMOLECULES PRINT GYRATION METAD UPPER_WALLS LOWER_WALLS CENTER MOLINFO | colvar function bias vatom isdb core generic |
20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | COORDINATIONNUMBER COMBINE LOWER_WALLS Q6 CENTER PAIRENTROPY PRINT DUMPGRID UNITS VOLUME CONVERT_TO_FES LOAD METAD REWEIGHT_METAD DISTANCE REWEIGHT_BIAS DENSITY COORDINATION CONTACT_MATRIX LOCAL_AVERAGE HISTOGRAM UPPER_WALLS FLUSH ENERGY SPRINT | adjmat colvar function volumes generic bias gridtools vatom setup sprint symfunc |
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 | SECONDARY_STRUCTURE_RMSD COMBINE BIASVALUE LOWER_WALLS ENDPLUMED GROUP WHOLEMOLECULES PRINT CS2BACKBONE PBMETAD CUSTOM ALPHABETA TORSION SUM ANTIBETARMSD LESS_THAN CONSTANT UPPER_WALLS FLUSH MOLINFO | secondarystructure colvar function bias isdb multicolvar core 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 | ABMD CONVERT_TO_FES COM READ PRINT LOWER_WALLS COMBINE METAD REWEIGHT_METAD UPPER_WALLS ENDPLUMED HISTOGRAM MATHEVAL DISTANCE DUMPGRID | colvar function bias gridtools vatom generic |
19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | RESTART COORDINATIONNUMBER DISTANCES ONES COMBINE ENDPLUMED CENTER GROUP PRINT UNITS CUSTOM MEAN SUM METAD DISTANCE MATRIX_VECTOR_PRODUCT CONTACT_MATRIX UPPER_WALLS FLUSH | symfunc adjmat colvar function generic matrixtools bias vatom core setup multicolvar |
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 | RESTART REWEIGHT_TEMP_PRESS CELL OPT_AVERAGED_SGD BF_LEGENDRE COMBINE LOWER_WALLS TD_WELLTEMPERED Q6 PRINT DUMPGRID VOLUME CONVERT_TO_FES LOAD TD_MULTITHERMAL_MULTIBARIC MATHEVAL REWEIGHT_BIAS READ HISTOGRAM ENERGY UPPER_WALLS OPT_DUMMY VES_LINEAR_EXPANSION | symfunc colvar function generic bias gridtools setup ves |
19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | COORDINATION CONVERT_TO_FES ANGLE PRINT OPT_AVERAGED_SGD LOWER_WALLS EXTERNAL COMBINE BF_CHEBYSHEV HISTOGRAM UPPER_WALLS TD_WELLTEMPERED FLUSH DUMPGRID DISTANCE TD_GRID UNITS VES_LINEAR_EXPANSION | colvar function generic bias gridtools setup ves |
19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | LOAD TORSION PRINT POSITION ENVIRONMENTSIMILARITY ENERGY ENDPLUMED Q6 UNITS | colvar envsim generic setup symfunc |
19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | RESTART CUSTOM GROUP DISTANCES COM ANGLE PRINT CENTER SUM FLUSH MOVINGRESTRAINT DISTANCE INPLANEDISTANCES | colvar function generic bias vatom core setup multicolvar |
19.044 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, water, density anomaly | Pablo Piaggi | RESTART REWEIGHT_TEMP_PRESS OPT_AVERAGED_SGD BF_LEGENDRE COMBINE PRINT AVERAGE DUMPGRID CUSTOM VOLUME CONVERT_TO_FES TD_MULTITHERMAL_MULTIBARIC REWEIGHT_BIAS ACCUMULATE READ HISTOGRAM ENERGY OPT_DUMMY VES_LINEAR_EXPANSION | colvar function ves bias gridtools setup generic |
19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | CUSTOM ALPHABETA TORSION PRINT CONSTANT COMBINE SUM FLUSH METAD COMMITTOR MOLINFO | colvar function bias multicolvar generic |
19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | GROUP COORDINATION CONVERT_TO_FES COM READ WHOLEMOLECULES PRINT FIT_TO_TEMPLATE METAD REWEIGHT_METAD UPPER_WALLS FLUSH HISTOGRAM MATHEVAL WRAPAROUND DUMPGRID ENDPLUMED POSITION | colvar function bias gridtools vatom core generic |
19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | GROUP PRINT BIASVALUE EMMI MOLINFO | isdb generic core bias |
19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | GROUP PRINT BIASVALUE EMMI MOLINFO | isdb generic core bias |
19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | INCLUDE GROUP ERMSD DISTANCES ANGLE PRINT LOWER_WALLS LOWEST COMBINE CENTER METAD FLUSH UPPER_WALLS RANDOM_EXCHANGES DISTANCE MOLINFO | colvar function bias vatom multicolvar core generic |
19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | RESTART LOAD TORSION PRINT POSITION VES_DELTA_F METAD ENERGY ENDPLUMED UNITS | colvar ves bias setup generic |