Browse the eggs in PLUMED-NEST
PLUMED-NEST provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation or analysis contained in a published paper. Furthermore, PLUMED-NEST monitors the compatibility of the provided PLUMED input files with the current and development versions of the code and integrates links from these files to the PLUMED manual.
Here is the list of projects already deposited in PLUMED-NEST, while a complete bibliography can be found here.
| plumID | Name | Category | Keywords | Contributor | Actions | Modules |
|---|---|---|---|---|---|---|
| 25.004 | Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride | chemistry | OPES, OPES flooding, Catalysis, Ammonia Synthesis | Axel Tosello Gardini | FLUSH UNITS GROUP COORDINATIONNUMBER FIXEDATOM OPES_METAD PRINT UPPER_WALLS CUSTOM DISTANCES ZDISTANCES DISTANCE COMMITTOR | colvar bias multicolvar core symfunc setup opes function vatom generic |
| 24.036 | Leveraging cryptic ligand envelopes through enhanced molecular simulations | bio | HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope | Francesco Colizzi | TORSION GROUP HISTOGRAM PRINT CONVERT_TO_FES DUMPGRID COORDINATION DISTANCE WHOLEMOLECULES ANGLE | core generic colvar gridtools |
| 24.033 | Transient interactions between the fuzzy coat and the cross-b core of brain-derived Ab42 filaments | bio | CryoEM, MEMMI, Metadynamics, Metainference, Ab42 Fibrils, structural ensemble | Maria Milanesi | CENTER GROUP RMSD UPPER_WALLS MOLINFO ALPHARMSD PRINT PARABETARMSD DUMPATOMS EMMI COORDINATION PBMETAD DUMPMASSCHARGE DISTANCE COM WHOLEMOLECULES BIASVALUE | colvar bias core vatom secondarystructure generic isdb |
| 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 | TORSION GROUP LOAD PRINT METAD COMMITTOR | colvar bias core setup generic |
| 24.018 | A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations | chemistry | prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning | Léon HUET | PRINT DISTANCE | generic colvar |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | UNITS CLUSTER_NATOMS COORDINATIONNUMBER PRINT UPPER_WALLS METAD DFSCLUSTERING CLUSTER_PROPERTIES CONTACT_MATRIX | adjmat bias setup symfunc clusters generic |
| 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 | FLUSH UNITS TORSION PRINT OPES_METAD UPPER_WALLS CUSTOM DISTANCE COMBINE LOWER_WALLS COMMITTOR | colvar bias setup opes function generic |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | CENTER FIXEDATOM PRINT UPPER_WALLS MOLINFO METAD RESTRAINT DUMPMASSCHARGE DISTANCE COMBINE | colvar bias function 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 | FIT_TO_TEMPLATE POSITION CUSTOM COORDINATION OPES_METAD_EXPLORE DISTANCE WRAPAROUND COMMITTOR ENDPLUMED UNITS ENERGY PRINT MOLINFO OPES_METAD COM LOWER_WALLS FLUSH CENTER TORSION GROUP UPPER_WALLS MATHEVAL WHOLEMOLECULES BIASVALUE | colvar bias setup opes core function vatom generic |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | OPES_EXPANDED TORSION ENERGY PRINT MOLINFO METAD OPES_METAD_EXPLORE DISTANCE ENDPLUMED ECV_MULTITHERMAL | generic opes colvar bias |
| 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 | CONTACTMAP FIXEDATOM FIT_TO_TEMPLATE CUSTOM COORDINATION DISTANCE ANGLE PYTORCH_MODEL COMMITTOR ENDPLUMED ENERGY RMSD OPES_METAD PRINT MOLINFO LOWER_WALLS CENTER GROUP UPPER_WALLS MATHEVAL COMBINE INCLUDE WHOLEMOLECULES | pytorch colvar bias core opes function vatom generic |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | PRINT METAD TORSION | generic colvar bias |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | PRINT METAD DISTANCES DISTANCE | generic colvar bias multicolvar |
| 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 | PRINT UPPER_WALLS METAD DRMSD CUSTOM CELL MATHEVAL LOWER_WALLS COMMITTOR | generic colvar bias function |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | CENTER LOAD GROUP ENERGY PRINT METAD COORDINATIONNUMBER VOLUME COMBINE INCLUDE | colvar bias setup core symfunc function vatom generic |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | KDE PRINT MATHEVAL DISTANCE COM TORSIONS | gridtools colvar multicolvar function vatom generic |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | FUNNEL_PS PRINT UPPER_WALLS METAD COM FUNNEL DISTANCE LOWER_WALLS | colvar bias vatom generic funnel |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | TORSION PRINT RESTART PBMETAD CONSTANT MATHEVAL WHOLEMOLECULES BIASVALUE | colvar bias setup function generic |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | PRINT ENDPLUMED TORSION | generic colvar |
| 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 | PRINT METAD TORSION DISTANCE | generic colvar bias |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | CENTER LOAD GROUP UPPER_WALLS METAD PRINT VOLUME INCLUDE | colvar bias setup core vatom generic |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | FLUSH UNITS TORSION GROUP LOAD PRINT OPES_METAD PYTORCH_MODEL UPPER_WALLS COM MATHEVAL DISTANCE LOWER_WALLS ENDPLUMED | pytorch colvar bias core opes setup function vatom generic |
| 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 | TD_WELLTEMPERED HISTOGRAM CONVERT_TO_FES VES_LINEAR_EXPANSION LOAD VOLUME DUMPGRID REWEIGHT_BIAS OPT_AVERAGED_SGD Q6 ENERGY READ PRINT RESTART LOWER_WALLS BF_LEGENDRE REWEIGHT_TEMP_PRESS UPPER_WALLS TD_MULTITHERMAL_MULTIBARIC OPT_DUMMY CELL MATHEVAL COMBINE | gridtools colvar ves bias setup symfunc function generic |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | TORSION PRINT RANDOM_EXCHANGES METAD INCLUDE | generic colvar bias |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | UNITS CENTER FOURIER_TRANSFORM GROUP FCCUBIC DUMPGRID MORE_THAN FIND_CONTOUR_SURFACE MULTICOLVARDENS | gridtools contour setup symfunc core function vatom fourier |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | FLUSH PATH UPPER_WALLS METAD RESTART PRINT DISTANCES | bias mapping multicolvar setup generic |
| 25.020 | Revealing Water-Mediated Activation Mechanisms in the Beta 1-Adrenergic Receptor via OneOPES-Enhanced Free Energy Landscapes | bio | OneOPES, GPCR, ADRB1, activation, microswitches, conformational changes, allostery | Valerio Rizzi | LOWER_WALLS GHOST OPES_METAD_EXPLORE ECV_MULTITHERMAL DISTANCE OPES_EXPANDED CUSTOM GROUP PATHMSD CENTER DISTANCES PRINT COORDINATION RMSD ENERGY UPPER_WALLS | bias opes vatom generic function multicolvar colvar core |
| 25.012 | A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis | bio | enzyme catalysis, transition state, structure-activity relationship, free energy surface, reaction mechanism, water, alpha-amylase, sugar, QM/MM MD, OPES, committor function, machine learning | Sudip Das | ENERGY LOAD COMBINE DISTANCE CUSTOM POSITION FLUSH BIASVALUE OPES_METAD INCLUDE CELL PRINT MATHEVAL COORDINATION TORSION UNITS | bias opes generic function colvar setup |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | RESTART DISTANCE CUSTOM HISTOGRAM METAD FLUSH REWEIGHT_METAD GROUP DUMPGRID PRINT COORDINATION UPPER_WALLS READ | bias gridtools generic function colvar setup core |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | VOLUME OPES_METAD_EXPLORE COMBINE RESTART ECV_MULTITHERMAL OPES_EXPANDED MOLINFO ERMSD PRINT COORDINATION ENERGY PYTORCH_MODEL | opes generic function pytorch colvar setup |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | LOWER_WALLS COMBINE DISTANCE POSITION MOLINFO METAD GROUP GYRATION DISTANCES CENTER WHOLEMOLECULES PRINT PUCKERING MATHEVAL GHOST UPPER_WALLS SORT | bias vatom generic function multicolvar colvar core |
| 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 | ENERGY DISTANCE OPES_METAD PRINT COORDINATION UPPER_WALLS | opes colvar generic bias |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | RESTART FLUSH METAD PRINT WHOLEMOLECULES TORSION | generic colvar setup bias |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | ECV_MULTITHERMAL OPES_EXPANDED MOLINFO CONTACTMAP INCLUDE PRINT WHOLEMOLECULES ENERGY UPPER_WALLS | opes colvar generic bias |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | DISTANCE CUSTOM POSITION FLUSH COM METAD GROUP DISTANCES CENTER PRINT WHOLEMOLECULES UNITS | bias vatom generic function multicolvar colvar setup core |
| 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 | SAXS WRAPAROUND DISTANCE ENSEMBLE MOLINFO BIASVALUE GROUP STATS CENTER PRINT RMSD UPPER_WALLS | bias isdb vatom generic function colvar core |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | COORDINATIONNUMBER LOWER_WALLS FIXEDATOM COMMITTOR DISTANCE CUSTOM FLUSH COM OPES_METAD GROUP DISTANCES PRINT MATHEVAL ENERGY UPPER_WALLS UNITS ZDISTANCES | bias symfunc opes vatom generic function multicolvar colvar setup core |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | PBMETAD COM GYRATION INCLUDE PRINT WHOLEMOLECULES COORDINATION RESTRAINT TORSION | generic colvar bias vatom |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | ECV_MULTITHERMAL OPES_EXPANDED CONTACTMAP ECV_UMBRELLAS_LINE PRINT WHOLEMOLECULES ENERGY | opes 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 | LOWER_WALLS METAD PRINT WHOLEMOLECULES PCAVARS UPPER_WALLS | generic bias mapping |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | COORDINATIONNUMBER LOAD COMBINE Q6 Q4 METAD PAIRENTROPY GROUP INCLUDE CENTER PRINT MATHEVAL | bias symfunc gridtools vatom generic function setup core |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | LOAD MOLINFO BIASVALUE EMMIVOX GROUP PRINT WHOLEMOLECULES | bias isdb generic setup core |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | OPT_AVERAGED_SGD VES_LINEAR_EXPANSION PRINT BF_FOURIER TD_UNIFORM TORSION | generic ves colvar |
| 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 VES_LINEAR_EXPANSION FLUSH BF_CUBIC_B_SPLINES PRINT COORDINATION TD_UNIFORM BF_CHEBYSHEV OPT_ADAM BF_LEGENDRE UNITS VES_OUTPUT_BASISFUNCTIONS ENERGY UPPER_WALLS DISTANCE BF_GAUSSIANS POSITION TD_WELLTEMPERED METAD INCLUDE BF_WAVELETS | ves bias generic colvar setup |
| 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 | FIXEDATOM METAD PRINT FIT_TO_TEMPLATE TORSION | generic colvar bias vatom |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | FIXEDATOM ENDPLUMED FLUSH PRINT RMSD COORDINATION GROUP DUMPGRID READ COM CONVERT_TO_FES MATHEVAL UPPER_WALLS DISTANCE POSITION HISTOGRAM METAD REWEIGHT_METAD WHOLEMOLECULES | bias gridtools vatom generic function colvar core |
| 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 | REWEIGHT_BIAS RESTART POSITION METAD CENTER PRINT MATHEVAL WHOLEMOLECULES COORDINATION RESTRAINT | bias vatom generic function colvar setup |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | LOWER_WALLS ENERGY DISTANCE MOLINFO HISTOGRAM METAD GROUP REWEIGHT_METAD DUMPGRID INCLUDE PRINT PUCKERING RANDOM_EXCHANGES WHOLEMOLECULES COORDINATION UPPER_WALLS | bias gridtools generic colvar core |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | HISTOGRAM MOLINFO BIASVALUE GROUP CONVERT_TO_FES DUMPGRID DISTANCES PRINT WHOLEMOLECULES RMSD EMMI READ | bias isdb gridtools generic multicolvar colvar core |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | FIXEDATOM ENDPLUMED DISTANCE UPPER_WALLS OPES_METAD GROUP CENTER PRINT FIT_TO_TEMPLATE MATHEVAL WHOLEMOLECULES ENERGY COORDINATION ANGLE PYTORCH_MODEL | bias opes vatom generic function pytorch colvar core |
| 20.012 | Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies | bio | metadynamics, well-tempered ensemble, ligand binding, binding affinity calculations, novel COLVAR, funnel restraints, Hamiltonian replica-exchange, PathCV, COMetPath, SWISH | Francesco Gervasio | LOWER_WALLS LOAD CONSTANT DISTANCE MOLINFO COM BIASVALUE METAD GROUP CONTACTMAP INCLUDE PRINT MATHEVAL WHOLEMOLECULES UPPER_WALLS PROJECTION_ON_AXIS FUNCPATHGENERAL | bias vatom generic function colvar setup core |
| 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 | PBMETAD LOWER_WALLS ENDPLUMED ANTIBETARMSD ALPHABETA CS2BACKBONE MOLINFO BIASVALUE FLUSH GROUP PRINT WHOLEMOLECULES UPPER_WALLS | bias isdb core generic multicolvar secondarystructure |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | DISTANCE MOLINFO METAD COM GYRATION PRINT ENERGY UPPER_WALLS | generic colvar bias vatom |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | REWEIGHT_BIAS COMMITTOR DISTANCE HISTOGRAM BIASVALUE METAD REWEIGHT_METAD CONVERT_TO_FES EXTERNAL DUMPGRID PRINT MATHEVAL TORSION READ | bias gridtools generic function colvar |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | POSITION MAZE_SIMULATED_ANNEALING MAZE_OPTIMIZER_BIAS MAZE_LOSS PRINT UNITS | maze generic colvar setup |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | COMBINE RESTART DISTANCE FLUSH METAD DISTANCES PRINT UPPER_WALLS UNITS | bias generic function multicolvar colvar setup |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | ENDPLUMED METAD PRINT MATHEVAL TORSION | generic colvar bias function |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | MFILTER_MORE DFSCLUSTERING ENDPLUMED OUTPUT_CLUSTER Q6 COMMITTOR CONTACT_MATRIX FLUSH CLUSTER_WITHSURFACE LOCAL_Q6 CLUSTER_NATOMS | symfunc clusters generic adjmat multicolvar |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | SAXS ENDPLUMED DISTANCE MOLINFO BIASVALUE GROUP STATS RESTRAINT INCLUDE CENTER PRINT WHOLEMOLECULES UPPER_WALLS RMSD | bias isdb vatom generic function colvar core |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | MOLINFO BIASVALUE GROUP PRINT EMMI | generic bias isdb core |
| 26.014 | Dissociation free energy (DFE) calculationsfor GPR15L–polySia | bio | metadynamics, protein-carbohydrate interaction | Davide Luciano and Gaston Courtade | PRINT METAD DISTANCE UPPER_WALLS COM GROUP | core vatom generic colvar bias |
| 26.008 | Ensemble Dynamics | methods | State Exploration, Protein Folding, Drug Binding, Phase Transition | Florian M. Dietrich | BIASVALUE OPES_METAD_EXPLORE PRINT UNITS GROUP LOAD CELL DISTANCE POSITION CUSTOM TORSION | core setup generic colvar function bias opes |
| 25.028 | Designing transferable transition state guided collective variable via interpretable machine learning model for enhanced sampling. A case study on polymer collapse transition | bio | metadynamics, polymer collapse transition, transferable CV,interpretable ML-model | Saikat Dhibar and Biman Jana | MATHEVAL PRINT METAD COORDINATION COMBINE GYRATION DISTANCE UPPER_WALLS CENTER LOWER_WALLS WHOLEMOLECULES GROUP | vatom core generic colvar function bias |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | PRINT GYRATION RESTRAINT DISTANCE PYTORCH_MODEL | pytorch bias colvar generic |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | FLUSH PRINT ABMD DISTANCE COM WHOLEMOLECULES COMMITTOR GROUP | core vatom generic colvar bias |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | METAD COMBINE ERMSD MOLINFO WHOLEMOLECULES | colvar bias generic function |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | FLUSH PRINT METAINFERENCE ENSEMBLE RDC STATS DISTANCE MOLINFO ALPHABETA WHOLEMOLECULES GROUP | core multicolvar generic colvar isdb function |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | FLUSH INCLUDE PARABETARMSD ALPHARMSD PRINT DIHCOR COORDINATION GROUP COMBINE GYRATION ENDPLUMED ANTIBETARMSD DISTANCE MOLINFO PBMETAD WHOLEMOLECULES TORSION | core multicolvar generic colvar function bias secondarystructure |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | INCLUDE POSITION LOWER_WALLS CUSTOM ENDPLUMED PRINT LOAD DISTANCE UPPER_WALLS BIASVALUE MATHEVAL UNITS COORDINATION CELL MOLINFO RMSD GROUP TORSION ENERGY WHOLEMOLECULES | core setup generic colvar function bias |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | PRINT UNITS METAD COMBINE DISTANCE WHOLEMOLECULES | setup generic colvar function bias |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | OPES_METAD_EXPLORE PRINT METAD COORDINATION DISTANCE UPPER_WALLS COM CENTER LOWER_WALLS CUSTOM WHOLEMOLECULES GROUP | vatom core generic colvar function bias opes |
| 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 | PRINT HISTOGRAM UPPER_WALLS OPES_EXPANDED DUMPGRID LOWER_WALLS ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY RESTART | gridtools generic envsim setup bias opes |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | MOVINGRESTRAINT ANGLE PRINT METAD DISTANCE UPPER_WALLS COM LOWER_WALLS WHOLEMOLECULES | vatom bias generic colvar |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | MFILTER_MORE Q4 PRINT LOCAL_Q4 DFSCLUSTERING COMBINE CLUSTER_NATOMS LOCAL_Q6 MFILTER_LESS Q6 COORDINATIONNUMBER CONTACT_MATRIX LOCAL_AVERAGE GROUP | core multicolvar symfunc clusters generic adjmat function |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | PRINT UNITS ECV_MULTITHERMAL ENERGY TORSION OPES_METAD POSITION OPES_EXPANDED ENDPLUMED | setup colvar generic opes |
| 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 | BIASVALUE FLUSH PATHMSD DRR METAD PRINT CUSTOM | drr generic colvar function 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 | PRINT METAD TORSION DISTANCE COM WHOLEMOLECULES GROUP | core vatom generic colvar bias |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | RMSD PRINT METAD COMBINE DISTANCE MOLINFO COM COORDINATIONNUMBER WHOLEMOLECULES COMMITTOR | vatom symfunc generic colvar function 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 | DISTANCE CENTER PRINT CONTACTMAP | vatom colvar generic |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | CONVERT_TO_FES INCLUDE PRINT METAD HISTOGRAM GROUP COMBINE GYRATION DISTANCES COM DUMPGRID REWEIGHT_BIAS | core gridtools multicolvar vatom generic colvar function bias |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | FLUSH MATHEVAL ANGLE PRINT COORDINATION GROUP LOAD ENERGY DISTANCE UPPER_WALLS FIT_TO_TEMPLATE FIXEDATOM CENTER PYTORCH_MODEL WHOLEMOLECULES COMMITTOR ENDPLUMED | core vatom pytorch setup generic colvar function bias |
| 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 | PRINT METAD GROUP GYRATION UPPER_WALLS ALPHABETA LOWER_WALLS WHOLEMOLECULES ENDPLUMED | core multicolvar generic colvar bias |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | PRINT GYRATION DISTANCE UPPER_WALLS MOLINFO COM PBMETAD | bias vatom colvar generic |
| 21.040 | A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms | bio | EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference | Faidon Brotzakis | BIASVALUE EMMI PRINT GROUP DISTANCE MOLINFO UPPER_WALLS COM WHOLEMOLECULES RESTART | core vatom generic setup isdb colvar bias |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | DISTANCE UPPER_WALLS LOWER_WALLS PRINT | bias colvar generic |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | INCLUDE PRINT METAD SAXS GYRATION ERMSD MOLINFO UPPER_WALLS LOWER_WALLS CUSTOM WHOLEMOLECULES GROUP | core generic isdb colvar function bias |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | FLUSH MOVINGRESTRAINT CONVERT_TO_FES UNITS PRINT METAD HISTOGRAM REWEIGHT_METAD LOAD UPPER_WALLS COORDINATIONNUMBER DUMPGRID COMMITTOR | gridtools symfunc setup generic bias |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | EEFSOLV BIASVALUE FLUSH ALPHARMSD PRINT SAXS METAINFERENCE GYRATION MOLINFO CENTER PBMETAD WHOLEMOLECULES GROUP | vatom core generic isdb colvar bias secondarystructure |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | PRINT DISTANCE COM WHOLEMOLECULES GROUP | core vatom colvar generic |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | TORSION PRINT METAD | bias colvar generic |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | MATHEVAL PRINT METAD ENERGY CELL UPPER_WALLS LOWER_WALLS VOLUME | colvar bias generic function |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | FLUSH PRINT UNITS METAD GROUP COMBINE UPPER_WALLS COORDINATIONNUMBER DISTANCES RESTART ENDPLUMED | core multicolvar symfunc setup generic function bias |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | MOVINGRESTRAINT UNITS PRINT GYRATION ENDPLUMED | generic bias setup colvar |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | PRINT METAD GROUP DISTANCE UPPER_WALLS COM CENTER LOWER_WALLS RESTART | vatom core generic setup colvar bias |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | BIASVALUE MATHEVAL INCLUDE ANGLE PRINT SAXS COORDINATION ENSEMBLE GROUP COMBINE STATS MOLINFO ALPHABETA CENTER PBMETAD WHOLEMOLECULES ENDPLUMED | core vatom multicolvar generic colvar isdb function bias |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | BIASVALUE MATHEVAL PRINT METAD DISTANCE UPPER_WALLS COM LOWER_WALLS WHOLEMOLECULES CONSTANT | vatom generic colvar function bias |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | PRINT RESTRAINT TORSION DISTANCE COM GROUP | core vatom generic colvar bias |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | PRINT METAD CELL UPPER_WALLS FUNCPATHMSD LOWER_WALLS PIV | piv generic colvar function bias |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | FLUSH PRINT METAD COMBINE MOLINFO ALPHABETA COMMITTOR | multicolvar bias generic function |
| 26.013 | Characterizing Partially Unfolded States of the C-Terminal Domain in WT and 3PA Mouse Prion Protein | bio | parallel-bias metadynamics, PBMetaD, metadynamics, mouse prion protein, prion protein, protein folding, partially unfolded states, molecular dynamics | Sonali M. Jadhav | GROUP COORDINATION ALPHARMSD GYRATION DISTANCE INCLUDE DUMPMASSCHARGE MOLINFO CONTACTMAP WHOLEMOLECULES PBMETAD COM PRINT | colvar secondarystructure vatom bias core generic |
| 26.002 | A Transferable and Robust Computational Framework for Class A GPCR Activation Free Energies | bio | OneOPES, GPCR, ADRB1, activation, euclidean path, microswitches, conformational changes, allostery | Valerio Rizzi | GROUP COORDINATION VOLUME OPES_EXPANDED CUSTOM LOWER_WALLS DISTANCE PATH ECV_MULTITHERMAL OPES_METAD_EXPLORE CENTER RMSD ENERGY PATHMSD PRINT UPPER_WALLS | colvar opes function mapping vatom bias core generic |
| 25.026 | Deciphering the Molecular Mechanisms of Startle Disease - the Role of the Asn46Lys Mutation in the Glycine Receptor | bio | metadynamics, glycine receptors, funnel metadynamics | Jacob Adam Clark | FUNNEL_PS METAD LOWER_WALLS FUNNEL COM PRINT UPPER_WALLS | generic bias vatom funnel |
| 25.014 | Atomic resolution ensembles of intrinsically disordered proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | GROUP BAIES BIASVALUE PRINT | bias core generic isdb |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | GROUP BIASVALUE METAD PYTORCH_MODEL LOWER_WALLS CUSTOM OPES_METAD ENDPLUMED DISTANCE POSITION MOLINFO UNITS WHOLEMOLECULES RMSD ENERGY TORSION PRINT UPPER_WALLS | colvar pytorch setup opes function bias core 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 | FIXEDATOM ANGLE RMSD UPPER_WALLS GROUP MATHEVAL COMMITTOR CUSTOM CONTACTMAP MOLINFO FIT_TO_TEMPLATE COORDINATION ENDPLUMED WHOLEMOLECULES TORSION PRINT METAD COMBINE DISTANCE OPES_METAD CENTER | colvar opes function vatom bias core generic |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | GROUP LOAD METAD COORDINATIONNUMBER INCLUDE CENTER PRINT | setup symfunc vatom bias core generic |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | BIASVALUE LOWER_WALLS CUSTOM POSITION OPES_METAD PYTORCH_MODEL ENDPLUMED UNITS PRINT UPPER_WALLS | colvar pytorch setup opes function bias generic |
| 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 | GROUP COORDINATION PYTORCH_MODEL CUSTOM LOWER_WALLS DISTANCE FIXEDATOM PATH OPES_METAD UNITS OPES_METAD_EXPLORE WHOLEMOLECULES FIT_TO_TEMPLATE TORSION CENTER PRINT UPPER_WALLS | colvar pytorch setup opes function mapping vatom bias core 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 | READ MATHEVAL HISTOGRAM METAD DISTANCE REWEIGHT_METAD MOLINFO WHOLEMOLECULES RMSD CONVERT_TO_FES DUMPGRID PRINT | gridtools colvar function bias generic |
| 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 | BIASVALUE MATHEVAL METAD LOWER_WALLS DISTANCE WHOLEMOLECULES CONSTANT PRINT UPPER_WALLS | function bias colvar generic |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | GROUP GYRATION MOLINFO WHOLEMOLECULES TORSION PBMETAD PRINT | bias colvar core generic |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | COORDINATION PYTORCH_MODEL CUSTOM UNITS OPES_METAD_EXPLORE PRINT | colvar pytorch setup opes function generic |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | TORSION WHOLEMOLECULES PRINT | colvar generic |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | BIASVALUE HISTOGRAM LOAD MOVINGRESTRAINT FLUSH REWEIGHT_BIAS COMMITTOR CUSTOM RESTRAINT COORDINATIONNUMBER UNITS VOLUME ANN CONVERT_TO_FES DUMPGRID PRINT UPPER_WALLS | gridtools colvar setup symfunc function annfunc bias generic |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | COORDINATION METAD ALPHARMSD DISTANCE INCLUDE CONTACTMAP MOLINFO UNITS RANDOM_EXCHANGES CENTER ANTIBETARMSD PRINT | colvar setup secondarystructure vatom bias generic |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | METAD COMMITTOR ENDPLUMED DISTANCE COORDINATIONNUMBER CENTER TORSION PRINT | colvar symfunc vatom bias generic |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | LOAD MOVINGRESTRAINT METAD COMBINE LOWER_WALLS CUSTOM RESTRAINT ENSEMBLE UNITS TORSION CONSTANT PRINT UPPER_WALLS | colvar setup function bias generic |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | INCLUDE RMSD GROUP OPES_EXPANDED CONTACTMAP MOLINFO UNITS ENERGY LOAD FLUSH PYTORCH_MODEL ENDPLUMED ECV_MULTITHERMAL WHOLEMOLECULES TORSION PRINT COMBINE Q6 DISTANCE OPES_METAD ENVIRONMENTSIMILARITY VOLUME | colvar pytorch setup symfunc envsim opes function core generic |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | GROUP COORDINATION UNITS WHOLEMOLECULES PBMETAD | colvar setup bias core generic |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | GROUP LOAD MFILTER_MORE CLUSTER_DISTRIBUTION FIXEDATOM COORDINATIONNUMBER RESTRAINT CONTACT_MATRIX DFSCLUSTERING DUMPGRID MULTICOLVARDENS AROUND DENSITY CLUSTER_NATOMS PRINT | gridtools volumes setup symfunc multicolvar clusters vatom bias adjmat core generic |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | GROUP BIASVALUE MATHEVAL FISST GYRATION DISTANCE RESTRAINT UNITS ENERGY PRINT | colvar fisst setup function bias core generic |
| 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 | COORDINATION METAD CUSTOM UNITS DISTANCES PRINT | colvar setup multicolvar function bias generic |
| 20.002 | Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study | bio | Metadynamics, path CVs | Riccardo Ocello | GROUP RESTART METAD MOLINFO WHOLEMOLECULES PATHMSD PRINT UPPER_WALLS | colvar setup bias 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 | READ MATHEVAL HISTOGRAM METAD COMBINE LOWER_WALLS ENDPLUMED DISTANCE REWEIGHT_METAD DUMPGRID CONVERT_TO_FES COM ABMD PRINT UPPER_WALLS | gridtools colvar function vatom bias generic |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | METAD DISTANCE MOLINFO WHOLEMOLECULES RMSD TORSION PRINT ERMSD | bias colvar generic |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | GROUP ENDPLUMED DISTANCE INCLUDE CENTER PRINT | vatom colvar core 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 METAD Q6 OUTPUT_CLUSTER SMAC CUSTOM CLUSTER_DISTRIBUTION COORDINATIONNUMBER CONTACT_MATRIX DFSCLUSTERING MORE_THAN MATRIX_VECTOR_PRODUCT ONES OUTER_PRODUCT CLUSTER_PROPERTIES DISTANCES CLUSTER_NATOMS PRINT | symfunc multicolvar clusters function matrixtools bias adjmat generic |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | MATHEVAL RESTART FLUSH METAD DISTANCE UNITS PRINT UPPER_WALLS | colvar setup function bias generic |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | METAD COMMITTOR LOWER_WALLS DISTANCE CENTER TORSION PRINT UPPER_WALLS | bias colvar vatom generic |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | RESTART METAD GYRATION ENDPLUMED COORDINATIONNUMBER DISTANCES PRINT | colvar setup symfunc multicolvar bias generic |
| 25.025 | Enhanced Sampling of Ligand Binding Coupled to RNA Conformational Dynamics | bio | OPES, OPES Flooding , Metadynamics, RNA, Ligand binding, Free Energy, Kinetics, Funnel | Revanth Elangovan and Dhiman Ray | WHOLEMOLECULES ENDPLUMED METAD COORDINATION MATHEVAL UPPER_WALLS GROUP CENTER TORSION OPES_METAD WRAPAROUND COM FUNNEL_PS FUNNEL LOWER_WALLS RMSD CUSTOM COMMITTOR PRINT DISTANCE | vatom opes bias generic funnel colvar function core |
| 25.022 | Imidazole Diffusion in SALEM-2 MOF | materials | OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials | Sudheesh Kumar Ethirajan | DISTANCES WHOLEMOLECULES GROUP UNITS CENTER PRINT ENDPLUMED OPES_METAD PROJECTION_ON_AXIS MOLINFO DISTANCE | vatom multicolvar setup opes generic colvar core |
| 25.019 | The Arch from the Stones. Understanding Protein Folding Energy Landscapes via Bio-inspired Collective Variables | bio | protein folding, OPES, OneOPES, binding free energy | Valerio Rizzi | RMSD OPES_METAD_EXPLORE CUSTOM OPES_EXPANDED GROUP CENTER COORDINATION COMBINE PRINT GHOST ECV_MULTITHERMAL MOLINFO DISTANCE ENERGY | vatom opes generic colvar function core |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | ENSEMBLE WHOLEMOLECULES FLUSH SAXS CENTER GYRATION PBMETAD METAINFERENCE PRINT TORSION UPPER_WALLS MOLINFO DISTANCE STATS | vatom generic bias colvar function isdb |
| 25.017 | Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity | bio | EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase | Samuel Hoff | WHOLEMOLECULES EMMIVOX GROUP BIASVALUE PRINT MOLINFO | core bias generic isdb |
| 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 | OPES_METAD_EXPLORE WHOLEMOLECULES OPES_EXPANDED FIT_TO_TEMPLATE GROUP CENTER PRINT UPPER_WALLS DISTANCE TORSION ENDPLUMED COORDINATION ECV_MULTITHERMAL MATHEVAL ANGLE FIXEDATOM LOWER_WALLS ENERGY | vatom opes bias generic colvar function core |
| 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 | FLUSH COMMITTOR RESTART BIASVALUE PRINT COORDINATIONNUMBER TORSION METAD MATHEVAL RESTRAINT MOLINFO DISTANCE ENERGY | setup bias generic colvar function symfunc |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | CUSTOM UNITS BIASVALUE PRINT DISTANCE | setup generic bias colvar function |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | WHOLEMOLECULES COM GYRATION PRINT MOVINGRESTRAINT TORSION INCLUDE COORDINATION ALPHABETA DISTANCE | multicolvar vatom bias generic colvar |
| 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 | PATHMSD ALPHARMSD FUNCPATHMSD INCLUDE PRINT DISTANCE METAD CONTACTMAP UPPER_WALLS MOLINFO LOWER_WALLS | generic bias colvar secondarystructure 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 | WHOLEMOLECULES EMMIVOX GROUP BIASVALUE PRINT INCLUDE UPPER_WALLS MOLINFO WRAPAROUND DISTANCE | bias generic isdb colvar core |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | Q4 VOLUME COMBINE PRINT COORDINATIONNUMBER METAD Q6 MATHEVAL ENERGY | generic bias colvar function symfunc |
| 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 WHOLEMOLECULES COMBINE BIASVALUE PRINT ERMSD METAD COORDINATION MOLINFO | function bias generic colvar |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | DISTANCES WHOLEMOLECULES FLUSH FIT_TO_TEMPLATE COM RESTART GROUP UNITS DUMPATOMS POSITION PRINT DISTANCE METAD MATHEVAL UPPER_WALLS WRAPAROUND LOWER_WALLS | vatom multicolvar setup generic bias colvar function core |
| 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 METAD CONTACTMAP UPPER_WALLS LOWER_WALLS ENERGY | bias generic colvar |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | WHOLEMOLECULES FLUSH GROUP GYRATION PRINT METAD COORDINATION UPPER_WALLS LOWER_WALLS | bias generic colvar core |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | ANTIBETARMSD WHOLEMOLECULES COM ALPHARMSD PBMETAD PRINT TORSION RESTART MOLINFO ALPHABETA | vatom multicolvar setup secondarystructure bias generic colvar |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | 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 | ENVIRONMENTSIMILARITY OPES_EXPANDED ECV_UMBRELLAS_LINE PRINT INCLUDE UPPER_WALLS LOWER_WALLS | generic bias envsim opes |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | RMSD DISTANCES BRIDGE WHOLEMOLECULES FLUSH FIT_TO_TEMPLATE ANGLE GROUP UNITS COMBINE PRINT DISTANCE METAD COORDINATION MATHEVAL UPPER_WALLS LOWER_WALLS | multicolvar setup generic bias adjmat colvar function core |
| 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 | WHOLEMOLECULES FLUSH ANGLE ALPHARMSD PRINT TORSION METAD COORDINATION UPPER_WALLS MOLINFO ALPHABETA DISTANCE | multicolvar bias generic colvar secondarystructure |
| 21.048 | Enhancing ligand exploration within a channel pore and fenestrations using metadynamics | bio | well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug | Elaine Tao | CUSTOM COM UNITS PRINT DISTANCE TORSION METAD UPPER_WALLS LOWER_WALLS | vatom setup generic bias colvar function |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | CLUSTER_DISTRIBUTION HISTOGRAM CONTACT_MATRIX DFSCLUSTERING CLUSTER_NATOMS GROUP COMBINE PRINT COORDINATIONNUMBER MFILTER_MORE LOCAL_Q6 METAD Q6 DUMPGRID INSPHERE FIXEDATOM | multicolvar vatom generic bias clusters adjmat gridtools volumes function symfunc core |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | DISTANCES WHOLEMOLECULES ENDPLUMED COORDINATION MATHEVAL UPPER_WALLS LOAD GROUP CENTER TORSION PYTORCH_MODEL OPES_METAD FIT_TO_TEMPLATE LOWER_WALLS UNITS PRINT ANGLE FIXEDATOM DISTANCE | multicolvar vatom setup opes bias generic pytorch colvar function core |
| 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 | WHOLEMOLECULES PATHMSD RESTART PRINT METAD UPPER_WALLS LOWER_WALLS | bias generic setup colvar |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | FIT_TO_TEMPLATE METAD CENTER PRINT RESTART DISTANCE | vatom setup bias generic colvar |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | CONVERT_TO_FES OPT_AVERAGED_SGD VES_LINEAR_EXPANSION HISTOGRAM FLUSH TD_GRID EXTERNAL UNITS BF_CHEBYSHEV COMBINE PRINT UPPER_WALLS COORDINATION TD_WELLTEMPERED ANGLE DUMPGRID LOWER_WALLS DISTANCE | ves setup bias generic gridtools colvar function |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | CUSTOM ANGLE GROUP CENTER COMBINE PRINT TORSION ENDPLUMED RESTRAINT DUMPDERIVATIVES DISTANCE | vatom generic bias colvar function core |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | ENVIRONMENTSIMILARITY UNITS POSITION PRINT TORSION ENDPLUMED Q6 LOAD ENERGY | envsim setup generic colvar symfunc |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | FLUSH UNITS COMBINE PRINT DISTANCE METAD UPPER_WALLS LOWER_WALLS ENERGY | setup bias generic colvar function |
| 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 | COM PRINT METAD UPPER_WALLS DISTANCE ENERGY | vatom bias generic colvar |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | WHOLEMOLECULES GYRATION PRINT TORSION METAD | bias generic colvar |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | GROUP BIASVALUE PRINT MOLINFO EMMI | generic bias isdb core |
| 26.004 | Resolving the ambiguous binding site of quercetin at the calcineurin subunit junction using funnel metadynamics with deep learning collective variables | bio | metadynamics, funnel metadynamics, DeepTICA | Jason Loo | WHOLEMOLECULES ENERGY DISTANCE RMSD PYTORCH_MODEL COORDINATION FUNNEL PRINT LOWER_WALLS MATHEVAL WRAPAROUND FUNNEL_PS UPPER_WALLS METAD GROUP COM | funnel pytorch vatom core colvar bias function generic |
| 25.029 | Energetic Constraints in the Enzymatic Depolymerization of Crystalline PET from enhanced molecular simulations | bio | HREX-Metadynamics, PETase, crystalline PET, amorphous PET, conformational ensembles, substrate binding, chain detachment | Ania Di Pede-Mattatelli and Francesco Colizzi | HISTOGRAM CONVERT_TO_FES DUMPGRID REWEIGHT_BIAS FIXEDATOM DISTANCE PRINT MOLINFO METAD LOWER_WALLS UPPER_WALLS WHOLEMOLECULES COM | vatom colvar bias gridtools generic |
| 25.023 | Molecular simulations of Tau-protein oligomers | bio | metadynamics, proteins, aggregation | Giovanni Bussi | HISTOGRAM CONVERT_TO_FES DUMPGRID CONTACTMAP REWEIGHT_BIAS CUSTOM RMSD RESTRAINT PRINT RESTART FLUSH METAD | setup colvar bias gridtools function generic |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | COMBINE OPES_METAD TORSION CUSTOM ENERGY DISTANCE PRINT COORDINATION LOAD GROUP | opes core colvar function setup generic |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | INCLUDE PRINT RESTART LOAD METAD GROUP | setup generic core bias |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | PBMETAD DISTANCE GYRATION PRINT COORDINATION UPPER_WALLS COM | vatom generic 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 | SKETCHMAP WHOLEMOLECULES PATHMSD LANDMARK_SELECT_FPS CUSTOM DISTANCE COLLECT_FRAMES PRINT VSTACK TRANSPOSE DISSIMILARITIES SKETCHMAP_PROJECTION VORONOI UPPER_WALLS METAD COM | landmarks vatom bias matrixtools colvar function dimred generic valtools |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | BIASVALUE PATHMSD CUSTOM PRINT LOWER_WALLS DRR UPPER_WALLS FLUSH METAD | drr bias colvar function generic |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | COMBINE BIASVALUE CUSTOM MOLINFO PRINT COORDINATION GHBFIX UPPER_WALLS FLUSH METAD GROUP LOAD | core colvar bias setup function generic |
| 22.027 | Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain | Max Bonomi | RMSD PRINT | generic colvar |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | PBMETAD DISTANCE GYRATION MOLINFO PRINT UPPER_WALLS COM | vatom generic colvar bias |
| 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 UNITS DISTANCE GYRATION COORDINATION COORDINATIONNUMBER LOWER_WALLS UPPER_WALLS FLUSH METAD COM | vatom symfunc colvar bias setup function 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 | PRINT LOAD WHOLEMOLECULES METAD | setup generic bias |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | COMBINE ENERGY TD_WELLTEMPERED PRINT VOLUME RESTART OPT_AVERAGED_SGD BF_LEGENDRE PAIRENTROPY VES_LINEAR_EXPANSION LOAD METAD | ves gridtools bias colvar function setup generic |
| 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 | COMBINE CUSTOM ENDPLUMED PRINT COORDINATION VOLUME METAD | bias generic colvar function |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | EXTERNAL TORSION ENERGY PRINT MOLINFO RESTART FLUSH | setup generic colvar bias |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | UNITS TD_WELLTEMPERED ANN COMBINE DUMPGRID REWEIGHT_BIAS BIASVALUE REWEIGHT_METAD CUSTOM RESTRAINT PRINT COORDINATIONNUMBER CONSTANT HISTOGRAM DISTANCE VES_LINEAR_EXPANSION UPPER_WALLS MOVINGRESTRAINT LOAD CONVERT_TO_FES OPES_METAD BF_CHEBYSHEV OPT_AVERAGED_SGD FLUSH METAD | opes annfunc ves bias symfunc colvar gridtools setup function generic |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | OPES_METAD TORSION ENDPLUMED OPES_EXPANDED ENERGY PRINT ECV_UMBRELLAS_LINE ECV_MULTITHERMAL | opes generic colvar |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | OPES_METAD PYTORCH_MODEL PRINT LOWER_WALLS MATHEVAL UPPER_WALLS FLUSH GROUP LOAD | opes pytorch bias core function setup 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 UNITS ENERGY DISTANCE DISTANCES PRINT LOWER_WALLS UPPER_WALLS LOAD GROUP | multicolvar bias core colvar function setup generic |
| 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 | Q6 OPT_DUMMY TD_WELLTEMPERED PRINT VOLUME RESTART ENVIRONMENTSIMILARITY OPT_AVERAGED_SGD BF_LEGENDRE MATHEVAL VES_LINEAR_EXPANSION UPPER_WALLS | ves envsim symfunc bias colvar function setup generic |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | ENDPLUMED DISTANCE RESTRAINT COORDINATION LOWER_WALLS WHOLEMOLECULES | generic colvar bias |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | FLUSH DISTANCES PRINT RESTART MOVINGRESTRAINT COM INPLANEDISTANCES | multicolvar vatom bias setup generic |
| 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 | POSITION UNITS PRINT COORDINATION RESTART LOWER_WALLS UPPER_WALLS FLUSH METAD GROUP | core colvar bias setup generic |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | PBMETAD BIASVALUE ENDPLUMED ANTIBETARMSD MOLINFO PRINT RESTART LOWER_WALLS ALPHABETA UPPER_WALLS FLUSH WHOLEMOLECULES GROUP CS2BACKBONE | multicolvar secondarystructure isdb core bias setup generic |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | DISTANCE PRINT METAD LOWER_WALLS UPPER_WALLS WHOLEMOLECULES COM | vatom generic colvar bias |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | TORSION DRR PRINT | generic drr colvar |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | COMBINE TORSION EDS DISTANCE RESTRAINT PRINT | eds colvar bias function generic |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | WHOLEMOLECULES ENDPLUMED ENERGY GYRATION MOLINFO PRINT METAD ALPHARMSD | secondarystructure generic colvar bias |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | WHOLEMOLECULES BIASVALUE TORSION PRINT MATHEVAL CONSTANT METAD | function generic colvar bias |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | INCLUDE BIASVALUE PUCKERING TORSION MOLINFO MATHEVAL CONSTANT | function generic colvar bias |
| 26.001 | Molecular simulations Alx riboswitch | bio | RNA, riboswitch | Giovanni Bussi | MOVINGRESTRAINT ERMSD DISTANCE RESTRAINT PRINT MATHEVAL MOLINFO | colvar function bias generic |
| 26.000 | OPES simulations of disordered proteins | bio | OPES, IDPs | Julian Streit | OPES_EXPANDED RESTART ENERGY ECV_MULTITHERMAL PRINT | colvar setup opes generic |
| 25.007 | Shaping the glycan landscape. Hidden relationships between linkage and ring distortion induced by carbohydrate-active enzmyes | bio | REST-RECT, REST2, glycan, enzyme, CAZyme, steered | Isabell Grothaus | TORSION MOVINGRESTRAINT METAD RESTRAINT PUCKERING DISTANCE RESTART PRINT MOLINFO | colvar setup bias generic |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | UPPER_WALLS METAD DISTANCE RESTART COM MOLINFO PRINT GROUP WHOLEMOLECULES FUNCPATHGENERAL | colvar setup bias generic core function vatom |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | POSITION PRINT UNITS RESTRAINT | colvar setup bias generic |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | TORSION METAD PUCKERING RESTART PRINT MOLINFO | colvar setup bias generic |
| 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 | UPPER_WALLS FLUSH PYTORCH_MODEL METAD PRINT DRR WHOLEMOLECULES MOLINFO COORDINATION RMSD LOWER_WALLS | colvar pytorch bias generic drr |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | COMMITTOR DISTANCE READ CONTACTMAP HISTOGRAM FIXEDATOM RMSD INCLUDE MATHEVAL PRINT FIT_TO_TEMPLATE CONVERT_TO_FES FLUSH PATH GROUP MOLINFO WRAPAROUND UPPER_WALLS REWEIGHT_METAD METAD COM ENDPLUMED WHOLEMOLECULES COORDINATION DUMPGRID | colvar mapping bias generic core function vatom gridtools |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | TORSION METAD RESTART PRINT UNITS | colvar setup bias generic |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | UPPER_WALLS DISTANCE COM GYRATION PRINT MOLINFO PBMETAD LOWER_WALLS | colvar generic bias vatom |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | METAD ALPHARMSD COMBINE POSITION PRINT WHOLEMOLECULES MOLINFO ANN FIT_TO_TEMPLATE | colvar bias generic annfunc secondarystructure function |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | ANGLE DISTANCE BIASVALUE CONSTANT MATHEVAL PRINT WHOLEMOLECULES PBMETAD | colvar function bias generic |
| 23.013 | Path meta-eABF simulation of large scale conformational change in STING protein | methods | meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint | Istvan Kolossvary | UPPER_WALLS FLUSH METAD TIME BIASVALUE PRINT DRR PATHMSD CUSTOM UNITS LOWER_WALLS | colvar setup bias generic function drr |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | ANGLE DUMPFORCES DISTANCE METAD ALPHARMSD COM CONTACTMAP PRINT MOLINFO | colvar bias generic secondarystructure vatom |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | CONVERT_TO_FES REWEIGHT_METAD METAD DISTANCE HISTOGRAM READ PRINT MATHEVAL WHOLEMOLECULES MOLINFO RMSD DUMPGRID | colvar bias generic function gridtools |
| 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 | TORSION METAD EXTRACV READ PRINT | colvar bias generic |
| 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 WHOLEMOLECULES MOLINFO PBMETAD | colvar bias generic |
| 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 | TORSION UPPER_WALLS RESTART COM BIASVALUE RMSD PRINT GROUP WHOLEMOLECULES MOLINFO COORDINATION PBMETAD EMMI | colvar setup bias generic core isdb vatom |
| 22.011 | Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck | methods | metadynamics, membrane permeation, protein folding | Shams Mehdi | UPPER_WALLS TORSION METAD DISTANCE ZANGLES COM COMBINE MATHEVAL YANGLES PRINT XANGLES WHOLEMOLECULES MOLINFO ALPHABETA CUSTOM LOWER_WALLS | colvar multicolvar bias generic function vatom |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | UPPER_WALLS PYTORCH_MODEL DISTANCE OPES_METAD COM PRINT OPES_METAD_EXPLORE MATHEVAL GROUP LOAD CUSTOM COORDINATION UNITS LOWER_WALLS | colvar opes pytorch setup bias generic core function vatom |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | TORSION UPPER_WALLS OPES_EXPANDED METAD OPES_METAD ENDPLUMED ENERGY ECV_UMBRELLAS_FILE ECV_MULTITHERMAL BIASVALUE PRINT OPES_METAD_EXPLORE POSITION CUSTOM UNITS PBMETAD LOWER_WALLS | colvar opes setup bias generic function |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | DISTANCE RESTRAINT PRINT GROUP LOAD FIXEDATOM | colvar setup bias generic core vatom |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | UPPER_WALLS METAD DISTANCE ALPHARMSD ENERGY INCLUDE MATHEVAL CONTACTMAP PRINT WHOLEMOLECULES MOLINFO LOWER_WALLS | colvar bias generic secondarystructure function |
| 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 | |
| 21.002 | Phase equilibrium of water with hexagonal and cubic ice using the SCAN functional | materials | ice, water, SCAN, OPES, VES, multithermal, crystallization, environment similarity, refcv, reweighting | Pablo Piaggi | BF_LEGENDRE OPT_AVERAGED_SGD UPPER_WALLS OPES_EXPANDED TD_UNIFORM RESTART ENERGY ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE PRINT VOLUME MATHEVAL ECV_MULTITHERMAL_MULTIBARIC VES_LINEAR_EXPANSION Q6 | colvar opes symfunc ves setup bias generic envsim function |
| 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 | TORSION ERMSD DISTANCE RESTART PRINT CENTER MOLINFO ABMD | colvar setup bias generic vatom |
| 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 COMBINE MOLINFO PRINT WHOLEMOLECULES STATS COORDINATION | colvar function bias generic |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | LOCAL_AVERAGE DISTANCE REWEIGHT_BIAS COORDINATIONNUMBER LOAD DENSITY HISTOGRAM UNITS CONTACT_MATRIX PAIRENTROPY PRINT VOLUME LOWER_WALLS CONVERT_TO_FES FLUSH UPPER_WALLS REWEIGHT_METAD METAD SPRINT COMBINE ENERGY CENTER COORDINATION Q6 DUMPGRID | colvar symfunc setup sprint bias generic adjmat function vatom volumes gridtools |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | TORSION UPPER_WALLS METAD DISTANCE RESTART COMBINE PRINT WHOLEMOLECULES MOLINFO RMSD | colvar setup bias generic function |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | UPPER_WALLS METAD RESTART PRINT PATHMSD UNITS LOWER_WALLS | colvar setup bias generic |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_SIMULATED_ANNEALING MAZE_LOSS PRINT POSITION MAZE_OPTIMIZER_BIAS UNITS | colvar setup maze generic |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | FUNCPATHMSD METAD DISTANCE COM ENDPLUMED CONTACTMAP PRINT WHOLEMOLECULES RMSD | colvar bias generic function vatom |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | TORSION COMMITTOR DISTANCE COM COMBINE RESTART PRINT EXTERNAL WHOLEMOLECULES ALPHABETA | colvar setup multicolvar bias generic function vatom |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | ERMSD METAD ENDPLUMED PRINT WHOLEMOLECULES MOLINFO RMSD | colvar bias generic |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | VES_DELTA_F TORSION METAD RESTART ENDPLUMED ENERGY PRINT POSITION LOAD UNITS | colvar ves setup bias generic |
| 26.012 | Buprenorphine Restricts the Conformational Landscape of the μ-Opioid Receptor | bio | OneOPES, GPCR, MOR, activation, euclidean path, conformational changes, allostery | Simone Aureli | ECV_MULTITHERMAL VOLUME CUSTOM COORDINATION PATH CENTER DISTANCE PRINT UPPER_WALLS RMSD OPES_EXPANDED ENERGY GROUP OPES_METAD_EXPLORE | bias core vatom opes mapping generic function colvar |
| 26.009 | Exploring the Conformational Landscape of HIV-1 TAR RNA by PT-WTE | bio | RNA, PT-WTE, HIV-1 TAR | Stefano Bosio | MOLINFO METAD WHOLEMOLECULES PRINT ENERGY GROUP | generic colvar core bias |
| 26.007 | Metadynamics Simulations Reveal the Protonation-Dependent Conformational Landscape of GSK-3β Dual Inhibitors | chemistry | metadynamics, ligand unbinding, path CVs, funnel metadynamics | Gian Marco Elisi | MOLINFO UNITS FUNNEL METAD ANGLE DISTANCE FUNNEL_PS WHOLEMOLECULES PATHMSD PRINT UPPER_WALLS COMBINE RMSD MATHEVAL COM LOWER_WALLS ENDPLUMED | bias setup vatom generic function colvar funnel |
| 25.030 | Committor Regularization | methods | metadynamics, enhanced sampling, mlcvs, committor, machine learning | Florian Dietrich | PRINT MOVINGRESTRAINT UNITS METAD | generic setup bias |
| 25.024 | Sampling glycan-glycan interactions for B22 calculations | bio | B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange | Isabell Louise Grothaus | RESTRAINT METAD DISTANCE PRINT COMBINE COM POSITION | bias vatom generic function colvar |
| 25.021 | All You Need Is Water. Converging Ligand Binding Simulations with Hydration Collective Variables | bio | OPES Explore, ligand binding, binding free energy, water, hydration CVs, SAMPL challenge, host-guest | Valerio Rizzi | FIXEDATOM ANGLE COORDINATION DISTANCE CENTER WHOLEMOLECULES FIT_TO_TEMPLATE PRINT UPPER_WALLS MATHEVAL ENERGY GROUP OPES_METAD_EXPLORE | bias core vatom opes generic function colvar |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | UNITS PATHMSD PRINT ABMD UPPER_WALLS ENDPLUMED | generic setup colvar bias |
| 24.035 | Data efficient machine learning potentials for modeling catalytic reactivity via active learning and enhanced sampling | chemistry | opes, catalysis, ammonia, machine learning potentials | Luigi Bonati | UNITS CUSTOM COORDINATION DISTANCE RESTART PRINT UPPER_WALLS COMMITTOR LOWER_WALLS GROUP OPES_METAD | bias core setup opes generic function colvar |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | FLUSH METAD CUSTOM DISTANCE INCLUDE MATHEVAL PYTORCH_MODEL ENDPLUMED MOLINFO UNITS WHOLEMOLECULES COMBINE RMSD POSITION GROUP OPES_METAD FIXEDATOM PRINT CONTACTMAP UPPER_WALLS ENERGY OPES_METAD_EXPLORE BIASVALUE COORDINATION CENTER FIT_TO_TEMPLATE LOWER_WALLS | bias core pytorch setup vatom opes generic function 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 | METAD CUSTOM INCLUDE OPES_EXPANDED MATHEVAL MOLINFO ECV_MULTITHERMAL WHOLEMOLECULES TORSION RMSD GROUP RESTART PROJECTION_ON_AXIS PRINT CONTACTMAP UPPER_WALLS COM ENERGY OPES_METAD_EXPLORE BIASVALUE COORDINATION CONSTANT WRAPAROUND LOWER_WALLS | bias core setup vatom opes generic function colvar |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | MOLINFO RESTRAINT BIASVALUE INCLUDE WHOLEMOLECULES PRINT ERMSD EMMIVOX GROUP | core bias generic isdb colvar |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | MOLINFO METAD BIASVALUE COORDINATION DISTANCE CENTER LOWER_WALLS GHBFIX PRINT UPPER_WALLS COMBINE COM DEBUG GROUP | bias core vatom generic function colvar |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | READ METAD DUMPGRID COORDINATION CONVERT_TO_FES HISTOGRAM PRINT COMMITTOR GROUP ENDPLUMED | core bias generic gridtools colvar |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | FIXEDATOM GROUP UNITS CLUSTER_NATOMS LOAD DUMPGRID RESTRAINT LOCAL_AVERAGE DENSITY COORDINATIONNUMBER DFSCLUSTERING HISTOGRAM PRINT AROUND CONTACT_MATRIX CLUSTER_DISTRIBUTION LOCAL_Q3 Q3 | adjmat core bias vatom setup volumes generic gridtools clusters symfunc |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | LOCAL_Q6 MFILTER_MORE METAD COORDINATIONNUMBER PRINT MOVINGRESTRAINT COMBINE Q6 LOWER_WALLS GROUP | bias core multicolvar generic function symfunc |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | ENVIRONMENTSIMILARITY INCLUDE PRINT UPPER_WALLS OPES_EXPANDED LOWER_WALLS RESTART ECV_UMBRELLAS_LINE | bias setup opes generic envsim |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | CUSTOM DISTANCE INCLUDE COMMITTOR PYTORCH_MODEL ENDPLUMED MOLINFO UNITS WHOLEMOLECULES TORSION COMBINE RMSD POSITION GROUP OPES_METAD PRINT CONTACTMAP ENERGY BIASVALUE CONSTANT | core bias pytorch setup opes generic function 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 | VOLUME DUMPGRID CUSTOM ENVIRONMENTSIMILARITY HISTOGRAM PRINT UPPER_WALLS AROUND ENERGY RESTART OPES_METAD | bias setup opes generic volumes gridtools function colvar envsim |
| 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 | MOLINFO ANTIBETARMSD METAD COORDINATION ALPHARMSD WHOLEMOLECULES PRINT RANDOM_EXCHANGES UPPER_WALLS GYRATION DIHCOR PARABETARMSD LOWER_WALLS GROUP ENERGY | bias core multicolvar generic secondarystructure colvar |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | RESTRAINT METAD INCLUDE PRINT MOVINGRESTRAINT UPPER_WALLS COMBINE CONSTANT | generic function bias |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | UNITS METAD DISTANCE WHOLEMOLECULES PRINT UPPER_WALLS COM LOWER_WALLS | bias setup vatom generic colvar |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | MOLINFO DISTANCE PRINT UPPER_WALLS GYRATION PBMETAD COM LOWER_WALLS ENERGY | generic vatom colvar bias |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | MOLINFO GROUP ALPHABETA METAD ALPHARMSD REWEIGHT_BIAS WHOLEMOLECULES PRINT CONTACTMAP PBMETAD RESTART | bias core setup multicolvar generic secondarystructure colvar |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | MOLINFO ANTIBETARMSD ALPHABETA METAD BIASVALUE CENTER WHOLEMOLECULES SAXS PRINT CONTACTMAP GYRATION TORSION STATS ENSEMBLE PBMETAD | bias vatom multicolvar generic secondarystructure function isdb colvar |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | COORDINATION CENTER WHOLEMOLECULES PRINT PBMETAD | generic vatom 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 | LOAD MOLINFO BIASVALUE WHOLEMOLECULES PRINT EMMIVOX DUMPATOMS GROUP | core bias setup generic isdb |
| 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 | FLUSH INCLUDE DIHCOR PBMETAD ENDPLUMED MOLINFO ANTIBETARMSD WHOLEMOLECULES TORSION COMBINE GROUP ALPHARMSD PRINT ENSEMBLE CS2BACKBONE METAINFERENCE COORDINATION STATS GYRATION PARABETARMSD | bias core multicolvar generic secondarystructure function isdb colvar |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | MOLINFO FLUSH METAD SORT DISTANCE INCLUDE WHOLEMOLECULES COORDINATION MAXENT PRINT TORSION MATHEVAL COM | bias vatom generic function colvar |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | UNITS METAD PRINT TORSION EXTERNAL POSITION ENDPLUMED OPES_METAD | bias setup opes generic colvar |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | RESTRAINT COMBINE COM POSITION ANN | bias vatom annfunc function colvar |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | METAD WHOLEMOLECULES PRINT GYRATION ENERGY | 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 | READ DUMPGRID METAD DISTANCE_FROM_CONTOUR REWEIGHT_BIAS CONVERT_TO_FES HISTOGRAM PRINT UPPER_WALLS COMBINE RESTART | bias setup generic contour gridtools function |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | MOLINFO ALPHABETA METAD WHOLEMOLECULES PRINT GYRATION UPPER_WALLS LOWER_WALLS GROUP | core bias multicolvar generic colvar |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | READ REWEIGHT_METAD FLUSH METAD DUMPGRID COORDINATION CONVERT_TO_FES WHOLEMOLECULES FIT_TO_TEMPLATE HISTOGRAM PRINT UPPER_WALLS WRAPAROUND MATHEVAL COM POSITION GROUP ENDPLUMED | bias core vatom generic gridtools function colvar |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | VOLUME METAD PRINT TORSION UPPER_WALLS COMBINE MATHEVAL LOWER_WALLS CELL ENERGY ENDPLUMED | generic function colvar bias |
| 26.010 | Solvation-Mediated Ammonia Synthesis in a Nanoheterogeneous Liquid Alloy | materials | OPES, Catalysis, Ammonia Synthesis | Axel Tosello Gardini | GROUP OPES_METAD_EXPLORE DISTANCE INCLUDE CUSTOM UNITS COORDINATIONNUMBER FLUSH UPPER_WALLS OPES_METAD DISTANCES PRINT COORDINATION | symfunc opes colvar setup bias function core generic multicolvar |
| 26.006 | Metadynamics simulations of buried phosphorylation sites and proline isomerisation | bio | metadynamics | Julian Streit | WHOLEMOLECULES MOLINFO TORSION METAD PRINT COORDINATION | bias colvar generic |
| 25.016 | Advancing in silico drug design with Bayesian refinement of AlphaFold models | bio | bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment | Samiran Sen | BIASVALUE BAIES GROUP PRINT | bias isdb generic core |
| 25.015 | Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY | materials | Molecular crystal, Force Field, Collective Variable | Pradip Si and Omar Valsson | DUMPMULTICOLVAR SMAC TORSIONS DISTANCES PRINT | symfunc multicolvar generic |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | MULTI_RMSD RESTART DISTANCE LOWER_WALLS MATHEVAL UNITS PBMETAD UPPER_WALLS PRINT | colvar setup bias function generic |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | WHOLEMOLECULES MOLINFO GROUP COMMITTOR DISTANCE TORSION MATHEVAL ENERGY CUSTOM PYTORCH_MODEL OPES_METAD COMBINE ENDPLUMED PRINT | pytorch opes colvar function core generic |
| 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 | WHOLEMOLECULES FIXEDATOM GROUP RESTART DISTANCE LOWER_WALLS FIT_TO_TEMPLATE TORSION CUSTOM CENTER PYTORCH_MODEL PATH UPPER_WALLS OPES_METAD PRINT COORDINATION | pytorch opes colvar setup bias function core mapping generic vatom |
| 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 | GROUP OPES_METAD_EXPLORE RESTART DISTANCE ECV_MULTITHERMAL TORSION ENERGY CUSTOM OPES_EXPANDED COMBINE PRINT COORDINATION | opes colvar setup function core generic |
| 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 | WHOLEMOLECULES MOLINFO ALPHARMSD DISTANCE TORSION CUSTOM GYRATION OPES_METAD COMBINE PRINT COORDINATION | opes colvar function generic secondarystructure |
| 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 MOLINFO DISTANCE MATHEVAL RMSD METAD PRINT | bias colvar function 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 DISTANCE LOWER_WALLS MATHEVAL CENTER UPPER_WALLS BIASVALUE METAD PRINT CONSTANT | colvar bias function generic vatom |
| 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 | SHADOW WRAPAROUND WHOLEMOLECULES MOLINFO GROUP FIT_TO_TEMPLATE CENTER POSITION UPPER_WALLS METAD DISTANCES PRINT | colvar bias isdb core generic vatom multicolvar |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | LOAD PRINT PBMETAD | bias setup generic |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | FIXEDATOM DISTANCE TORSION MATHEVAL CUSTOM CENTER UPPER_WALLS METAD PRINT | colvar bias function generic vatom |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | COM DISTANCE CUSTOM UNITS FLUSH BIASVALUE METAD DRR PRINT | colvar setup drr bias function generic vatom |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | MOLINFO PUCKERING HISTOGRAM CONVERT_TO_FES TORSION DUMPGRID METAD READ PRINT | gridtools colvar bias generic |
| 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 | WHOLEMOLECULES GROUP FIXEDATOM COMMITTOR DISTANCE LOWER_WALLS FIT_TO_TEMPLATE MATHEVAL RMSD CENTER CUSTOM PYTORCH_MODEL UPPER_WALLS OPES_METAD PRINT COORDINATION | pytorch opes colvar bias function core generic vatom |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | WHOLEMOLECULES MOLINFO ERMSD BIASVALUE COMBINE METAD PRINT COORDINATION | bias colvar function 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 | COM DISTANCE TORSION INCLUDE ALPHABETA ENERGY GYRATION PBMETAD METAD PRINT COORDINATION | colvar bias generic vatom multicolvar |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | WHOLEMOLECULES COM DISTANCE UNITS UPPER_WALLS PATHMSD METAD PRINT | colvar setup bias generic vatom |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | EXTERNAL UNITS COORDINATIONNUMBER DUMPGRID REWEIGHT_METAD PRINT REWEIGHT_BIAS RESTRAINT TD_GRID HISTOGRAM CONVERT_TO_FES BF_CHEBYSHEV VES_LINEAR_EXPANSION UWALLS LOWER_WALLS FLUSH METAD LOAD DISTANCE OPT_AVERAGED_SGD ANGLES UPPER_WALLS COMBINE DISTANCES COORDINATION | symfunc colvar setup bias function ves gridtools generic multicolvar |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | WHOLEMOLECULES MOLINFO GROUP RESTRAINT DISTANCE STATS INCLUDE CENTER SAXS ENSEMBLE BIASVALUE PRINT | colvar bias isdb function core generic vatom |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | MULTI_RMSD RESTRAINT HISTOGRAM CONVERT_TO_FES DUMPGRID METAD REWEIGHT_METAD PRINT | bias gridtools colvar generic |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | WHOLEMOLECULES MOLINFO DIHCOR INCLUDE ALPHABETA GYRATION PBMETAD PRINT COORDINATION | bias colvar multicolvar generic |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | WHOLEMOLECULES MOLINFO DISTANCE STATS TORSION ALPHABETA CENTER GYRATION METAINFERENCE SAXS FLUSH PBMETAD ENSEMBLE PRINT | colvar bias isdb function generic vatom multicolvar |
| 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 | MOLINFO ABMD CONTACTMAP DUMPGRID REWEIGHT_METAD PRINT WHOLEMOLECULES HISTOGRAM CONVERT_TO_FES FUNCPATHMSD READ ENDPLUMED LOWER_WALLS FLUSH METAD COM DISTANCE UPPER_WALLS COMBINE | colvar bias function gridtools generic vatom |
| 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 | LOWER_WALLS ENERGY GYRATION COORDINATIONNUMBER UPPER_WALLS METAD DISTANCES ENDPLUMED PRINT | symfunc colvar bias generic multicolvar |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | MOLINFO COM DISTANCE ENERGY GYRATION UPPER_WALLS METAD PRINT | vatom bias colvar generic |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | WHOLEMOLECULES LOWER_WALLS UPPER_WALLS PATHMSD METAD PRINT | bias colvar generic |
| 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 | WHOLEMOLECULES MOLINFO GROUP BRIDGE COM DISTANCE LOWER_WALLS TORSION RMSD FUNNEL ALPHABETA DISTANCES UPPER_WALLS COMBINE METAD REWEIGHT_METAD PRINT | colvar bias function core generic vatom adjmat multicolvar funnel |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | DISTANCE ENERGY UNITS FLUSH UPPER_WALLS COMBINE METAD PRINT | colvar setup bias function generic |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | WHOLEMOLECULES COM DISTANCE LOWER_WALLS RMSD FUNNEL UPPER_WALLS METAD FUNNEL_PS PRINT | colvar bias generic vatom funnel |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | WHOLEMOLECULES MOLINFO GROUP BIASVALUE EMMI PRINT | bias isdb core generic |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | WHOLEMOLECULES MOLINFO CS2BACKBONE GROUP DISTANCE INCLUDE ALPHABETA GYRATION METAINFERENCE CENTER PBMETAD PRINT COORDINATION | colvar bias isdb core generic vatom multicolvar |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | WHOLEMOLECULES MOLINFO CS2BACKBONE GROUP RDC METAINFERENCE PRINT | isdb core generic |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | MOLINFO DISTANCE ERMSD LOWER_WALLS INCLUDE RANDOM_EXCHANGES ANGLE FLUSH UPPER_WALLS COMBINE METAD DISTANCES PRINT | colvar bias function generic multicolvar |
| 26.011 | Lets Stalk About Membranes. Committor-Based Enhanced Sampling of Stalk Formation. | bio | committor, machine learning, enhanced sampling, OPES, membrane fusion, stalk formation, nanoparticles | Giorgia Rossi | BIASVALUE CENTER PRINT GROUP CUSTOM LOWER_WALLS LOAD OPES_METAD_EXPLORE COORDINATION | setup function colvar core opes generic bias vatom |
| 25.027 | Enhanced-sampling MD simulations of a protein-peptide complex integrating SAXS and XL-MS experimental information | bio | steered MD, metadynamics, SAXS, XL-MS, ensemble reconstruction | Mattia Bernetti | CENTER PRINT GYRATION METAD GROUP DISTANCE WHOLEMOLECULES MOLINFO UPPER_WALLS INCLUDE SAXS MOVINGRESTRAINT | colvar core generic isdb bias vatom |
| 25.005 | Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations | chemistry | WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD | Vikas Tiwari, Tarak Karmakar | UNITS COORDINATIONNUMBER RESTRAINT FIXEDATOM PRINT METAD DISTANCES ANGLE GROUP COMBINE DISTANCE LOWER_WALLS UPPER_WALLS FLUSH COORDINATION COM | setup function colvar core generic multicolvar bias vatom symfunc |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | UNITS PRINT METAD GROUP TORSION | setup colvar core generic 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 | UNITS COORDINATIONNUMBER OPES_METAD PRINT FIXEDATOM GROUP DISTANCE UPPER_WALLS FLUSH ZDISTANCES | setup colvar core opes generic multicolvar bias vatom symfunc |
| 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 METAD SUM MATHEVAL INCLUDE FLUSH TRANSPOSE SELECT_COMPONENTS | function valtools generic matrixtools bias |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | PRINT PBMETAD GYRATION DISTANCE UPPER_WALLS COM | vatom colvar bias generic |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | PRINT METAD COMBINE DISTANCE WHOLEMOLECULES UPPER_WALLS FLUSH TORSION COM | function colvar generic bias vatom |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | UNITS PIV PRINT Q6 PAIRENTROPY RESTRAINT METAD VOLUME CUSTOM UPPER_WALLS Q4 ENERGY LOCAL_AVERAGE FUNCPATHMSD | setup function piv colvar gridtools generic bias symfunc |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | PRINT FUNNEL_PS PATHMSD FUNNEL METAD DISTANCE LOWER_WALLS WHOLEMOLECULES UPPER_WALLS COM | colvar funnel generic bias vatom |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | DISTANCE CENTER PRINT | generic colvar vatom |
| 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 RMSD PRINT | colvar generic |
| 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 | PRINT ENDPLUMED PBMETAD METAD RANDOM_EXCHANGES INCLUDE TORSION | colvar bias generic |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | PRINT ENDPLUMED VOLUME UPPER_WALLS OPES_EXPANDED RMSD ECV_LINEAR Q6 ECV_MULTITHERMAL_MULTIBARIC CUSTOM MOLINFO LOAD ENVIRONMENTSIMILARITY ENERGY TORSION UNITS ECV_MULTITHERMAL POSITION WHOLEMOLECULES MATHEVAL ECV_UMBRELLAS_LINE | setup function colvar opes generic envsim bias symfunc |
| 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 STATS WHOLEMOLECULES MOLINFO COORDINATION | colvar function bias generic |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | CENTER PRINT DISTANCES GROUP DISTANCE RESTART WHOLEMOLECULES COORDINATION | setup colvar core generic multicolvar vatom |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | CENTER RMSD PRINT METAD COMBINE DISTANCE LOWER_WALLS WHOLEMOLECULES MOLINFO UPPER_WALLS ENERGY MATHEVAL | function colvar generic bias vatom |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | UNITS COORDINATIONNUMBER PRINT ENDPLUMED EXTERNAL METAD GROUP COMBINE RESTART FLUSH | setup function core generic bias symfunc |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | UNITS FCCUBIC PRINT ENDPLUMED METAD UPPER_WALLS CELL | setup colvar generic bias symfunc |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | UNITS FCCUBIC PRINT ENDPLUMED METAD LOWER_WALLS UPPER_WALLS CELL AROUND | setup colvar generic bias symfunc volumes |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | METAINFERENCE JCOUPLING ENSEMBLE BIASVALUE PRINT PBMETAD ENDPLUMED GYRATION STATS CS2BACKBONE WHOLEMOLECULES MOLINFO FLUSH RDC TORSION | function colvar generic isdb bias |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | EXTERNAL METAD GROUP COORDINATION ENERGY | core colvar bias |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | ALPHABETA METAINFERENCE ENSEMBLE CENTER DIHCOR PRINT DHENERGY PBMETAD ENDPLUMED STATS RESTRAINT GROUP DISTANCE WHOLEMOLECULES MOLINFO UPPER_WALLS RDC TORSION | function colvar core generic multicolvar isdb bias vatom |