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 |
|---|---|---|---|---|---|---|
| 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 | LOWER_WALLS GROUP LOAD BIASVALUE OPES_METAD_EXPLORE CUSTOM CENTER COORDINATION PRINT | vatom setup function opes generic bias core colvar |
| 26.001 | Molecular simulations Alx riboswitch | bio | RNA, riboswitch | Giovanni Bussi | MATHEVAL MOLINFO ERMSD DISTANCE RESTRAINT MOVINGRESTRAINT PRINT | bias generic function colvar |
| 25.024 | Sampling glycan-glycan interactions for B22 calculations | bio | B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange | Isabell Louise Grothaus | COM COMBINE METAD DISTANCE RESTRAINT POSITION PRINT | vatom function generic bias 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 | GROUP MATHEVAL FIT_TO_TEMPLATE OPES_METAD_EXPLORE FIXEDATOM UPPER_WALLS ENERGY CENTER DISTANCE WHOLEMOLECULES ANGLE COORDINATION PRINT | vatom function opes generic bias core 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 | CONSTANT WRAPAROUND OPES_METAD_EXPLORE CUSTOM COM METAD ENERGY CONTACTMAP TORSION BIASVALUE UPPER_WALLS WHOLEMOLECULES LOWER_WALLS MATHEVAL RMSD MOLINFO RESTART COORDINATION INCLUDE GROUP ECV_MULTITHERMAL PROJECTION_ON_AXIS OPES_EXPANDED PRINT | vatom setup function opes generic bias core colvar |
| 23.043 | Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling | materials | Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters | Lorenzo Gigli | MATHEVAL SUM FLUSH SELECT_COMPONENTS METAD INCLUDE PRINT TRANSPOSE | function valtools generic bias matrixtools |
| 23.031 | Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN | bio | RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites | Max Bonomi | GROUP FIT_TO_TEMPLATE WRAPAROUND DISTANCES MOLINFO UPPER_WALLS METAD CENTER WHOLEMOLECULES POSITION PRINT SHADOW | vatom generic bias multicolvar isdb core colvar |
| 23.009 | Deep Learning Collective Variables from Transition Path Ensemble | methods | TPI-Deep-TDA, Deep-TDA, Transition Path, OPES, OPES Flooding, Machine Learning, Protein folding, Ligand binding | Dhiman Ray | CUSTOM ENERGY CENTER COMMITTOR PYTORCH_MODEL CONTACTMAP ENDPLUMED UPPER_WALLS ANGLE WHOLEMOLECULES LOWER_WALLS MATHEVAL FIT_TO_TEMPLATE RMSD MOLINFO COMBINE COORDINATION INCLUDE GROUP FIXEDATOM DISTANCE PRINT OPES_METAD | vatom function generic opes pytorch bias core colvar |
| 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 | EXTRACV TORSION READ METAD PRINT | bias generic colvar |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | METAD TORSION PRINT | bias generic colvar |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | LOWER_WALLS GROUP GYRATION FLUSH UPPER_WALLS METAD WHOLEMOLECULES COORDINATION PRINT | bias core colvar generic |
| 22.011 | Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck | methods | metadynamics, membrane permeation, protein folding | Shams Mehdi | LOWER_WALLS MATHEVAL XANGLES YANGLES TORSION CUSTOM ZANGLES MOLINFO ALPHABETA COM UPPER_WALLS COMBINE METAD DISTANCE WHOLEMOLECULES PRINT | vatom function generic bias multicolvar colvar |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | BIASVALUE MOLINFO COMBINE METAD ERMSD WHOLEMOLECULES COORDINATION PRINT | bias generic function colvar |
| 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 | CUSTOM ENDPLUMED COMBINE METAD VOLUME COORDINATION PRINT | bias generic function colvar |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | GROUP LOAD MULTICOLVARDENS CLUSTER_DISTRIBUTION MFILTER_MORE FIXEDATOM DUMPGRID CLUSTER_NATOMS AROUND DFSCLUSTERING COORDINATIONNUMBER RESTRAINT CONTACT_MATRIX DENSITY PRINT | vatom setup gridtools generic clusters volumes bias adjmat multicolvar symfunc core |
| 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 | |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | LOWER_WALLS GROUP LOAD MATHEVAL FLUSH UPPER_WALLS PYTORCH_MODEL PRINT OPES_METAD | setup function generic opes pytorch bias core |
| 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 MOLINFO RESTART METAD UPPER_WALLS PATHMSD WHOLEMOLECULES PRINT | setup generic bias core colvar |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | MATHEVAL MAXENT FLUSH TORSION MOLINFO COM METAD DISTANCE WHOLEMOLECULES COORDINATION INCLUDE PRINT SORT | vatom function generic bias colvar |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | MATHEVAL TORSION REWEIGHT_METAD BIASVALUE READ DUMPGRID METAD HISTOGRAM CONVERT_TO_FES DISTANCE REWEIGHT_BIAS COMMITTOR EXTERNAL PRINT | function gridtools generic bias colvar |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | LOWER_WALLS UNITS UPPER_WALLS METAD RESTART PATHMSD PRINT | bias setup colvar generic |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | GROUP MULTICOLVARDENS UNITS DUMPGRID MORE_THAN CENTER FCCUBIC FOURIER_TRANSFORM FIND_CONTOUR_SURFACE | vatom setup function gridtools contour symfunc core fourier |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | TORSION ALPHABETA COM COMBINE RESTART DISTANCE WHOLEMOLECULES EXTERNAL COMMITTOR PRINT | vatom setup function generic bias multicolvar colvar |
| 26.005 | Cryptic pocket discovery in Alzheimer disease risk proteins BIN1, PICALM, and CD2AP via well-tempered metadynamics | methods | cryptic pockets, Alzheimer disease, BIN1, PICALM, CD2AP, well-tempered metadynamics, endocytosis, clathrin-mediated trafficking, virtual screening | Cagrı Ozkurt | METAD ANGLE DISTANCE PRINT WHOLEMOLECULES | bias generic colvar |
| 25.027 | Enhanced-sampling MD simulations of a protein-peptide complex integrating SAXS and XL-MS experimental information | bio | steered MD, metadynamics, SAXS, XL-MS, ensemble reconstruction | Mattia Bernetti | CENTER GROUP UPPER_WALLS METAD MOLINFO INCLUDE SAXS MOVINGRESTRAINT DISTANCE PRINT WHOLEMOLECULES GYRATION | core isdb generic colvar bias vatom |
| 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 | ENERGY CENTER COMBINE GHOST OPES_METAD_EXPLORE GROUP MOLINFO COORDINATION ECV_MULTITHERMAL DISTANCE PRINT CUSTOM RMSD OPES_EXPANDED | core generic colvar opes function vatom |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | MULTI_RMSD RESTART LOWER_WALLS PBMETAD DISTANCE UNITS UPPER_WALLS PRINT MATHEVAL | generic colvar bias function setup |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | ABMD ENDPLUMED PATHMSD UNITS UPPER_WALLS PRINT | bias generic colvar setup |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | ENERGY COMBINE RESTART PYTORCH_MODEL OPES_METAD_EXPLORE MOLINFO ERMSD COORDINATION ECV_MULTITHERMAL PRINT VOLUME OPES_EXPANDED | generic colvar opes pytorch function setup |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | PUCKERING RESTART TORSION METAD MOLINFO PRINT | bias generic colvar setup |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | TORSION ALPHABETA DISTANCE MOVINGRESTRAINT COORDINATION COM INCLUDE PRINT WHOLEMOLECULES GYRATION | multicolvar generic colvar bias vatom |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | PBMETAD LOWER_WALLS MOLINFO DISTANCE COM UPPER_WALLS PRINT GYRATION | bias generic colvar vatom |
| 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 | COMBINE METAD MOLINFO BIASVALUE ERMSD GHBFIX COORDINATION PRINT WHOLEMOLECULES | bias colvar generic function |
| 23.029 | An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations | bio | SAXS, SANS, SAS, metainference, proteins, nucleic-acid | Federico Ballabio | RMSD CENTER GROUP MOLINFO DISTANCE SAXS BIASVALUE WRAPAROUND UPPER_WALLS PRINT STATS ENSEMBLE | core isdb generic colvar bias function vatom |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | DUMPATOMS RESTART POSITION GROUP LOWER_WALLS FIT_TO_TEMPLATE METAD DISTANCE UNITS FLUSH WRAPAROUND COM UPPER_WALLS PRINT MATHEVAL WHOLEMOLECULES DISTANCES | core multicolvar generic colvar bias function vatom setup |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | TORSION GROUP PBMETAD MOLINFO PRINT WHOLEMOLECULES GYRATION | core generic colvar bias |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | DUMPGRID CONVERT_TO_FES HISTOGRAM READ METAD MOLINFO REWEIGHT_METAD DISTANCE PRINT MATHEVAL WHOLEMOLECULES RMSD | generic colvar bias function gridtools |
| 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 | RESTART LOWER_WALLS UPPER_WALLS HISTOGRAM ENVIRONMENTSIMILARITY DUMPGRID ECV_UMBRELLAS_LINE PRINT OPES_EXPANDED | generic bias opes envsim gridtools setup |
| 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 | bias multicolvar generic colvar |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | PUCKERING TORSION CONVERT_TO_FES HISTOGRAM READ METAD MOLINFO DUMPGRID PRINT | bias gridtools generic colvar |
| 22.020 | Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA | bio | RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics | Weiwei He | TORSION GROUP METAD COM DISTANCE PRINT WHOLEMOLECULES | core generic colvar bias vatom |
| 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 | CENTER OPES_METAD COMMITTOR PYTORCH_MODEL GROUP LOWER_WALLS FIXEDATOM FIT_TO_TEMPLATE CUSTOM DISTANCE COORDINATION UPPER_WALLS PRINT MATHEVAL WHOLEMOLECULES RMSD | core generic colvar opes pytorch bias function vatom |
| 22.012 | Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT | bio | contact maps, protein-protein interactions | Isabell-Louise Grothaus | CENTER CONTACTMAP PRINT DISTANCE | generic colvar vatom |
| 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 | ALPHARMSD TORSION ALPHABETA METAD MOLINFO DISTANCE FLUSH ANGLE COORDINATION UPPER_WALLS PRINT WHOLEMOLECULES | multicolvar generic colvar bias secondarystructure |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | OPES_METAD ENERGY TORSION OPES_METAD_EXPLORE PBMETAD ENDPLUMED POSITION LOWER_WALLS METAD UNITS BIASVALUE ECV_MULTITHERMAL UPPER_WALLS PRINT ECV_UMBRELLAS_FILE CUSTOM OPES_EXPANDED | generic colvar opes bias function setup |
| 21.048 | Enhancing ligand exploration within a channel pore and fenestrations using metadynamics | bio | well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug | Elaine Tao | TORSION LOWER_WALLS METAD DISTANCE UNITS COM UPPER_WALLS PRINT CUSTOM | generic colvar bias function vatom setup |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | COORDINATIONNUMBER CENTER ENERGY COMBINE GROUP METAD INCLUDE PRINT VOLUME LOAD | core symfunc generic colvar bias function vatom setup |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | GROUP PBMETAD UNITS COORDINATION WHOLEMOLECULES | core generic colvar bias setup |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | ENERGY RESTART TORSION MOLINFO FLUSH EXTERNAL PRINT | bias generic colvar setup |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | COORDINATIONNUMBER CONVERT_TO_FES BIASVALUE DUMPGRID PRINT CUSTOM BF_CHEBYSHEV COMBINE HISTOGRAM OPT_AVERAGED_SGD UPPER_WALLS REWEIGHT_METAD LOAD METAD FLUSH CONSTANT MOVINGRESTRAINT VES_LINEAR_EXPANSION DISTANCE ANN OPES_METAD RESTRAINT UNITS TD_WELLTEMPERED REWEIGHT_BIAS | symfunc generic colvar annfunc bias opes setup function gridtools ves |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | GROUP LOWER_WALLS METAD MOLINFO INCLUDE SAXS ERMSD UPPER_WALLS PRINT WHOLEMOLECULES CUSTOM GYRATION | core isdb generic colvar bias function |
| 21.015 | Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin | bio | metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module | Gaston Courtade | CENTER RESTART POSITION RESTRAINT MATHEVAL METAD COORDINATION PRINT WHOLEMOLECULES REWEIGHT_BIAS | generic colvar bias function vatom setup |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | CENTER TORSION ENSEMBLE ALPHABETA PBMETAD METAD ANTIBETARMSD MOLINFO CONTACTMAP SAXS BIASVALUE PRINT WHOLEMOLECULES STATS GYRATION | isdb multicolvar generic colvar bias secondarystructure function 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 CONVERT_TO_FES HISTOGRAM METAD DUMPGRID PRINT REWEIGHT_METAD | bias gridtools generic colvar |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | DIHCOR PBMETAD ALPHABETA MOLINFO COORDINATION INCLUDE PRINT WHOLEMOLECULES GYRATION | bias multicolvar generic colvar |
| 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 | CONVERT_TO_FES MOLINFO DUMPGRID PRINT COMBINE ABMD FUNCPATHMSD LOWER_WALLS ENDPLUMED HISTOGRAM COM UPPER_WALLS REWEIGHT_METAD WHOLEMOLECULES METAD CONTACTMAP FLUSH DISTANCE READ | generic colvar bias function vatom gridtools |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | OPES_METAD PYTORCH_MODEL TORSION GROUP ENDPLUMED UPPER_WALLS LOWER_WALLS UNITS FLUSH COM DISTANCE PRINT MATHEVAL LOAD | core generic colvar opes pytorch bias function vatom setup |
| 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 | COORDINATIONNUMBER ENERGY LOWER_WALLS ENDPLUMED METAD UPPER_WALLS PRINT GYRATION DISTANCES | symfunc multicolvar generic colvar bias |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | ENERGY METAD PRINT WHOLEMOLECULES GYRATION | bias generic colvar |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | LOWER_WALLS ENDPLUMED CELL METAD UNITS UPPER_WALLS PRINT AROUND FCCUBIC | symfunc generic colvar bias setup volumes |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | TORSION GROUP RESTRAINT COM DISTANCE PRINT | core generic colvar bias vatom |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | PIV FUNCPATHMSD LOWER_WALLS CELL METAD UPPER_WALLS PRINT | generic colvar piv bias function |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | TORSION METAD CONSTANT BIASVALUE PRINT MATHEVAL WHOLEMOLECULES | bias function generic colvar |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | DIHCOR CENTER DHENERGY METAINFERENCE TORSION GROUP ALPHABETA PBMETAD ENDPLUMED RESTRAINT MOLINFO DISTANCE UPPER_WALLS PRINT WHOLEMOLECULES STATS RDC ENSEMBLE | core isdb multicolvar generic colvar bias function vatom |
| 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 | PRINT UNITS MOLINFO UPPER_WALLS MATHEVAL ENDPLUMED PATHMSD LOWER_WALLS COMBINE COM ANGLE WHOLEMOLECULES FUNNEL_PS METAD RMSD FUNNEL DISTANCE | colvar generic function funnel bias setup 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 | GROUP COORDINATIONNUMBER DISTANCES UPPER_WALLS FIXEDATOM PRINT COORDINATION LOWER_WALLS COMBINE RESTRAINT COM ANGLE METAD FLUSH UNITS DISTANCE | core colvar symfunc generic function setup bias multicolvar vatom |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | GROUP PRINT SORT MOLINFO POSITION DISTANCES UPPER_WALLS MATHEVAL GYRATION LOWER_WALLS COMBINE PUCKERING GHOST DISTANCE WHOLEMOLECULES METAD CENTER | core colvar bias generic function multicolvar vatom |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | PRINT CUSTOM BIASVALUE UNITS DISTANCE | colvar generic function bias setup |
| 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 | GROUP COORDINATIONNUMBER PRINT UPPER_WALLS FIXEDATOM ZDISTANCES FLUSH OPES_METAD UNITS DISTANCE | core colvar generic symfunc setup bias multicolvar vatom opes |
| 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 | PRINT MOLINFO UPPER_WALLS INCLUDE PATHMSD LOWER_WALLS FUNCPATHMSD ALPHARMSD METAD CONTACTMAP DISTANCE | colvar generic function secondarystructure bias |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | GROUP PRINT HISTOGRAM COORDINATION ENDPLUMED READ CONVERT_TO_FES METAD COMMITTOR DUMPGRID | core colvar generic gridtools bias |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | PRINT CONSTANT PBMETAD MATHEVAL ANGLE WHOLEMOLECULES BIASVALUE DISTANCE | generic function colvar bias |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | PRINT DRR COM CUSTOM FLUSH METAD BIASVALUE UNITS DISTANCE | colvar generic function bias drr setup vatom |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | CUSTOM PRINT CONSTANT TORSION UPPER_WALLS MOVINGRESTRAINT LOWER_WALLS COMBINE RESTRAINT METAD LOAD UNITS ENSEMBLE | colvar generic function bias setup |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | PRINT MOLINFO UPPER_WALLS PBMETAD GYRATION COM DISTANCE | generic vatom colvar bias |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | GROUP PRINT FIXEDATOM RESTRAINT LOAD DISTANCE | core colvar generic bias setup vatom |
| 21.030 | Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains | bio | parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure | Jim Pfaendtner | ALPHABETA PRINT TORSION PBMETAD ENERGY COORDINATION GYRATION INCLUDE COM METAD DISTANCE | colvar generic bias multicolvar vatom |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | ALPHABETA PRINT TORSION MOLINFO PBMETAD GYRATION SAXS STATS DISTANCE WHOLEMOLECULES METAINFERENCE FLUSH ENSEMBLE CENTER | colvar generic function isdb bias multicolvar vatom |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | PRINT TORSION RANDOM_EXCHANGES INCLUDE METAD | generic colvar bias |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | PRINT POSITION MAZE_OPTIMIZER_BIAS MAZE_LOSS MAZE_SIMULATED_ANNEALING UNITS | generic setup colvar maze |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | PRINT UPPER_WALLS ENDPLUMED FCCUBIC METAD CELL UNITS | colvar symfunc generic bias setup |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | GROUP PRINT MOLINFO EMMI BIASVALUE | generic core isdb bias |
| 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 | METAD ENDPLUMED DISTANCE GROUP CENTER OPES_METAD LOWER_WALLS COM FUNNEL TORSION CUSTOM RMSD PRINT WHOLEMOLECULES UPPER_WALLS COMMITTOR MATHEVAL FUNNEL_PS COORDINATION WRAPAROUND | function bias vatom funnel core generic opes colvar |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | CUSTOM PYTORCH_MODEL ENERGY LOWER_WALLS MOLINFO METAD PRINT RMSD WHOLEMOLECULES UNITS ENDPLUMED UPPER_WALLS DISTANCE GROUP BIASVALUE POSITION TORSION OPES_METAD | function bias setup generic core opes pytorch colvar |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | FUNCPATHGENERAL COM METAD MOLINFO WHOLEMOLECULES UPPER_WALLS PRINT RESTART DISTANCE GROUP | function bias setup vatom generic core colvar |
| 24.036 | Leveraging cryptic ligand envelopes through enhanced molecular simulations | bio | HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope | Francesco Colizzi | DUMPGRID ANGLE HISTOGRAM CONVERT_TO_FES PRINT WHOLEMOLECULES COORDINATION DISTANCE GROUP TORSION | gridtools core colvar generic |
| 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 COMBINE PARABETARMSD MOLINFO WHOLEMOLECULES COORDINATION PRINT ALPHARMSD INCLUDE GYRATION DISTANCE GROUP DIHCOR ENDPLUMED TORSION PBMETAD ANTIBETARMSD | function multicolvar bias secondarystructure core generic colvar |
| 24.014 | Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation | methods | data augmentation, geodesic interpolation, collective variables, protein folding | Juno Nam | FLUSH PYTORCH_MODEL LOWER_WALLS DRR METAD RMSD UPPER_WALLS COORDINATION PRINT MOLINFO WHOLEMOLECULES | bias generic pytorch colvar drr |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | FLUSH METAD WHOLEMOLECULES PRINT RESTART TORSION | bias colvar generic setup |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | ENERGY MOLINFO PRINT WHOLEMOLECULES UPPER_WALLS INCLUDE CONTACTMAP OPES_EXPANDED ECV_MULTITHERMAL | bias colvar generic opes |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | UNITS METAD UPPER_WALLS COORDINATIONNUMBER PRINT DFSCLUSTERING CLUSTER_PROPERTIES CONTACT_MATRIX CLUSTER_NATOMS | clusters setup bias generic symfunc adjmat |
| 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 | CUSTOM FLUSH COMBINE LOWER_WALLS UNITS PRINT UPPER_WALLS DISTANCE COMMITTOR TORSION OPES_METAD | function bias setup generic opes colvar |
| 23.041 | Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference | methods | EMMIVox, cryo-EM, single-structure refinement, ensemble refinement, Bayesian inference, B-factors, structural ensembles | Samuel Hoff | MOLINFO PRINT WHOLEMOLECULES EMMIVOX UPPER_WALLS INCLUDE BIASVALUE DISTANCE GROUP WRAPAROUND | bias isdb generic core colvar |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | COMBINE ENERGY MATHEVAL VOLUME METAD PRINT COORDINATIONNUMBER Q4 Q6 | function bias generic colvar symfunc |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | COM PRINT UPPER_WALLS GYRATION DISTANCE PBMETAD | bias vatom generic colvar |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | RESTRAINT COM WHOLEMOLECULES COORDINATION PRINT GYRATION INCLUDE TORSION PBMETAD | bias vatom generic colvar |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | LOWER_WALLS ANGLE COM METAD PRINT WHOLEMOLECULES UPPER_WALLS DISTANCE MOVINGRESTRAINT | bias vatom colvar generic |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | TORSION WHOLEMOLECULES PRINT | colvar 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 | colvar generic |
| 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 | CUSTOM DUMPGRID ENERGY VOLUME HISTOGRAM UPPER_WALLS AROUND PRINT RESTART ENVIRONMENTSIMILARITY OPES_METAD | gridtools function bias setup generic opes colvar volumes envsim |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | COMBINE COM MOLINFO RMSD WHOLEMOLECULES PRINT METAD COORDINATIONNUMBER DISTANCE COMMITTOR | function bias vatom generic colvar symfunc |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | METAD UNITS MOLINFO COORDINATION PRINT ALPHARMSD INCLUDE RANDOM_EXCHANGES DISTANCE CENTER ANTIBETARMSD CONTACTMAP | bias setup vatom secondarystructure generic colvar |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | DISTANCE CENTER PRINT | vatom colvar generic |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | COMBINE ENERGY VOLUME METAD PRINT LOAD RESTART OPT_AVERAGED_SGD PAIRENTROPY BF_LEGENDRE VES_LINEAR_EXPANSION TD_WELLTEMPERED | gridtools ves function bias setup generic colvar |
| 21.046 | Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs | bio | wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder | Elena Papaleo | LOWER_WALLS METAD ALPHABETA WHOLEMOLECULES UPPER_WALLS PRINT GYRATION ENDPLUMED GROUP | multicolvar bias core generic colvar |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | DUMPGRID FIXEDATOM COMBINE MFILTER_MORE INSPHERE HISTOGRAM CONTACT_MATRIX METAD DFSCLUSTERING PRINT COORDINATIONNUMBER LOCAL_Q6 GROUP CLUSTER_DISTRIBUTION CLUSTER_NATOMS Q6 | gridtools function multicolvar clusters bias vatom generic core volumes symfunc adjmat |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | FLUSH PYTORCH_MODEL LOAD ENDPLUMED DISTANCE GROUP CONTACTMAP OPES_METAD OPES_EXPANDED Q6 COMBINE ENERGY INCLUDE TORSION UNITS RMSD PRINT MOLINFO WHOLEMOLECULES VOLUME ENVIRONMENTSIMILARITY ECV_MULTITHERMAL | function setup core generic opes pytorch colvar symfunc envsim |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | FLUSH DUMPGRID HISTOGRAM REWEIGHT_METAD CONVERT_TO_FES UNITS METAD PRINT COORDINATIONNUMBER UPPER_WALLS LOAD COMMITTOR MOVINGRESTRAINT | gridtools bias setup generic symfunc |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | FLUSH METAD DENSITY LOAD COORDINATIONNUMBER DISTANCE CENTER SPRINT Q6 DUMPGRID COMBINE ENERGY LOWER_WALLS LOCAL_AVERAGE REWEIGHT_BIAS HISTOGRAM UNITS UPPER_WALLS PRINT PAIRENTROPY VOLUME CONVERT_TO_FES REWEIGHT_METAD COORDINATION CONTACT_MATRIX | gridtools function sprint bias setup vatom generic colvar symfunc volumes adjmat |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | ENERGY MATHEVAL FISST RESTRAINT UNITS PRINT GYRATION BIASVALUE DISTANCE GROUP | function bias setup fisst generic core colvar |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | MOLINFO PRINT LOAD EMMIVOX WHOLEMOLECULES DUMPATOMS BIASVALUE GROUP | setup isdb bias core 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 | MATHEVAL OPT_DUMMY VOLUME PRINT UPPER_WALLS RESTART TD_WELLTEMPERED ENVIRONMENTSIMILARITY OPT_AVERAGED_SGD BF_LEGENDRE VES_LINEAR_EXPANSION Q6 | ves function bias setup generic colvar symfunc envsim |
| 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 | FLUSH LOWER_WALLS MOLINFO ALPHABETA WHOLEMOLECULES UPPER_WALLS PRINT ENDPLUMED BIASVALUE GROUP ANTIBETARMSD CS2BACKBONE PBMETAD | multicolvar bias isdb secondarystructure core generic |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | ENERGY COM METAD MOLINFO UPPER_WALLS PRINT GYRATION DISTANCE | bias vatom colvar generic |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | FLUSH COMBINE ENERGY UNITS METAD UPPER_WALLS PRINT DISTANCE | function setup bias generic colvar |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | MATHEVAL METAD PRINT ENDPLUMED TORSION | bias function colvar generic |
| 26.010 | Solvation-Mediated Ammonia Synthesis in a Nanoheterogeneous Liquid Alloy | materials | OPES, Catalysis, Ammonia Synthesis | Axel Tosello Gardini | OPES_METAD_EXPLORE COORDINATIONNUMBER OPES_METAD CUSTOM UNITS COORDINATION FLUSH GROUP INCLUDE PRINT DISTANCE DISTANCES UPPER_WALLS | function core colvar setup multicolvar bias opes symfunc generic |
| 26.009 | Exploring the Conformational Landscape of HIV-1 TAR RNA by PT-WTE | bio | RNA, PT-WTE, HIV-1 TAR | Stefano Bosio | MOLINFO WHOLEMOLECULES ENERGY GROUP PRINT METAD | core colvar bias generic |
| 25.030 | Committor Regularization | methods | metadynamics, enhanced sampling, mlcvs, committor, machine learning | Florian Dietrich | MOVINGRESTRAINT METAD PRINT UNITS | bias setup generic |
| 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 | GYRATION WHOLEMOLECULES CENTER LOWER_WALLS COORDINATION GROUP MATHEVAL PRINT DISTANCE METAD COMBINE UPPER_WALLS | core vatom function colvar bias generic |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | GYRATION RESTRAINT PYTORCH_MODEL PRINT DISTANCE | colvar bias pytorch generic |
| 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 | OPES_METAD CUSTOM POSITION COORDINATION UNITS ENERGY FLUSH DISTANCE INCLUDE PRINT CELL MATHEVAL BIASVALUE LOAD COMBINE TORSION | function colvar setup bias opes generic |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | READ HISTOGRAM DUMPGRID CUSTOM COORDINATION GROUP FLUSH PRINT RESTART DISTANCE REWEIGHT_METAD METAD UPPER_WALLS | core function colvar setup bias gridtools generic |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | MOLINFO WHOLEMOLECULES ERMSD METAD COMBINE | colvar bias function generic |
| 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 | OPES_METAD CUSTOM LOWER_WALLS UNITS COORDINATION GROUP COMMITTOR PRINT RESTART DISTANCE UPPER_WALLS | function core colvar setup bias opes generic |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | RESTRAINT PRINT POSITION UNITS | bias colvar setup generic |
| 24.033 | Transient interactions between the fuzzy coat and the cross-b core of brain-derived Ab42 filaments | bio | CryoEM, MEMMI, Metadynamics, Metainference, Ab42 Fibrils, structural ensemble | Maria Milanesi | MOLINFO ALPHARMSD DUMPATOMS WHOLEMOLECULES CENTER COM PBMETAD EMMI PARABETARMSD COORDINATION GROUP DUMPMASSCHARGE PRINT RMSD BIASVALUE DISTANCE UPPER_WALLS | isdb core vatom colvar bias secondarystructure generic |
| 24.021 | Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state | chemistry | ion pairing, caco3, opes, proton transfer, crystallization | Pablo Piaggi | OPES_METAD COORDINATION ENERGY PRINT DISTANCE UPPER_WALLS | colvar bias opes generic |
| 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 | MOLINFO RESTART COORDINATIONNUMBER RESTRAINT ENERGY COMMITTOR FLUSH MATHEVAL PRINT BIASVALUE DISTANCE METAD TORSION | function colvar setup bias symfunc generic |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | CUSTOM LOWER_WALLS COORDINATION ENDPLUMED PRINT RMSD DISTANCE TORSION POSITION MATHEVAL CELL BIASVALUE LOAD UPPER_WALLS MOLINFO WHOLEMOLECULES UNITS ENERGY GROUP INCLUDE | function core colvar setup bias generic |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | DUMPGRID COM FIT_TO_TEMPLATE REWEIGHT_METAD HISTOGRAM CONTACTMAP COORDINATION PATH ENDPLUMED FLUSH PRINT RMSD DISTANCE READ WRAPAROUND FIXEDATOM COMMITTOR MATHEVAL CONVERT_TO_FES UPPER_WALLS MOLINFO WHOLEMOLECULES GROUP INCLUDE METAD | function vatom core colvar bias gridtools generic mapping |
| 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 MOLINFO HISTOGRAM DUMPGRID WHOLEMOLECULES MATHEVAL PRINT RMSD CONVERT_TO_FES DISTANCE REWEIGHT_METAD METAD | function colvar bias gridtools generic |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | OPES_METAD_EXPLORE WHOLEMOLECULES CENTER COM CUSTOM LOWER_WALLS COORDINATION GROUP PRINT DISTANCE METAD UPPER_WALLS | function vatom core colvar bias opes 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 | DRR PATHMSD CUSTOM TIME LOWER_WALLS UNITS FLUSH PRINT BIASVALUE METAD UPPER_WALLS | drr function colvar setup bias generic |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | DRR PATHMSD CUSTOM LOWER_WALLS FLUSH PRINT BIASVALUE METAD UPPER_WALLS | drr function colvar 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 | WHOLEMOLECULES LOWER_WALLS MATHEVAL PRINT BIASVALUE DISTANCE METAD UPPER_WALLS CONSTANT | bias function generic colvar |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | ECV_UMBRELLAS_LINE LOWER_WALLS OPES_EXPANDED INCLUDE PRINT RESTART ENVIRONMENTSIMILARITY UPPER_WALLS | setup bias opes generic envsim |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | GYRATION MOLINFO COM PBMETAD PRINT DISTANCE UPPER_WALLS | colvar bias generic vatom |
| 22.001 | Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials | methods | enhanced sampling, variationally enhanced sampling, ves, metadynamics, bias representation, wavelets, adam | Benjamin Pampel | BF_GAUSSIANS BF_CUBIC_B_SPLINES BF_CHEBYSHEV COORDINATION OPT_AVERAGED_SGD FLUSH PRINT DISTANCE TD_UNIFORM POSITION BF_WAVELETS VES_OUTPUT_BASISFUNCTIONS UPPER_WALLS TD_WELLTEMPERED VES_LINEAR_EXPANSION BF_LEGENDRE UNITS ENERGY INCLUDE OPT_ADAM METAD | ves colvar setup bias generic |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | CENTER COORDINATIONNUMBER ENDPLUMED COMMITTOR PRINT DISTANCE METAD TORSION | vatom colvar bias symfunc generic |
| 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 FIT_TO_TEMPLATE PRINT METAD TORSION | bias colvar generic vatom |
| 21.034 | Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics | bio | reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics | Dongdong Wang | RANDOM_EXCHANGES PBMETAD ENDPLUMED INCLUDE PRINT METAD TORSION | bias colvar generic |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | ECV_MULTITHERMAL OPES_METAD ENDPLUMED OPES_EXPANDED ENERGY PRINT ECV_UMBRELLAS_LINE TORSION | colvar opes generic |
| 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 LOWER_WALLS PRINT RESTART METAD UPPER_WALLS | colvar bias setup generic |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | WHOLEMOLECULES CENTER COORDINATION GROUP PRINT RESTART DISTANCE DISTANCES | core vatom colvar setup multicolvar 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 HISTOGRAM DUMPGRID COM ABMD LOWER_WALLS ENDPLUMED MATHEVAL PRINT CONVERT_TO_FES DISTANCE REWEIGHT_METAD METAD COMBINE UPPER_WALLS | function vatom colvar bias gridtools generic |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | UNITS FLUSH MATHEVAL PRINT RESTART DISTANCE METAD UPPER_WALLS | function colvar setup bias generic |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | WHOLEMOLECULES COM LOWER_WALLS PRINT DISTANCE METAD UPPER_WALLS | bias colvar generic vatom |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | GYRATION WHOLEMOLECULES PRINT METAD TORSION | colvar bias generic |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | MOLINFO WHOLEMOLECULES EMMI GROUP PRINT BIASVALUE | core bias isdb generic |
| 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 | RMSD COORDINATION LOWER_WALLS GROUP FUNNEL_PS PYTORCH_MODEL PRINT COM FUNNEL UPPER_WALLS WHOLEMOLECULES DISTANCE MATHEVAL WRAPAROUND METAD ENERGY | funnel bias function colvar core pytorch generic vatom |
| 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 | RMSD COORDINATION GROUP PATHMSD LOWER_WALLS PRINT CUSTOM OPES_METAD_EXPLORE DISTANCE VOLUME ECV_MULTITHERMAL CENTER OPES_EXPANDED UPPER_WALLS PATH ENERGY | bias function opes mapping colvar core generic vatom |
| 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 PRINT GROUP BAIES | isdb core bias generic |
| 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 PRINT TORSIONS SMAC DISTANCES | multicolvar symfunc 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 | PRINT MOVINGRESTRAINT DISTANCE RESTRAINT RESTART TORSION MOLINFO METAD PUCKERING | setup colvar bias generic |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | ALPHABETA GROUP MOLINFO METAINFERENCE PRINT RDC FLUSH STATS WHOLEMOLECULES DISTANCE ENSEMBLE | function colvar core generic multicolvar isdb |
| 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 | COORDINATION FIT_TO_TEMPLATE CENTER FIXEDATOM DISTANCE ANGLE MOLINFO UPPER_WALLS METAD RMSD GROUP COMBINE PRINT COMMITTOR WHOLEMOLECULES ENDPLUMED MATHEVAL TORSION CONTACTMAP OPES_METAD CUSTOM | bias function opes colvar core generic vatom |
| 24.019 | Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning | bio | OPES, machine learning, protein folding, adaptive sampling | Mingyuan Zhang | ALPHARMSD COORDINATION COMBINE PRINT GYRATION WHOLEMOLECULES DISTANCE TORSION MOLINFO OPES_METAD CUSTOM | secondarystructure function opes colvar generic |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | DEBUG COORDINATION GROUP LOWER_WALLS COMBINE BIASVALUE PRINT COM GHBFIX DISTANCE METAD CENTER MOLINFO UPPER_WALLS | bias function colvar core generic vatom |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | INCLUDE GROUP LOAD PRINT RESTART METAD | setup core bias 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 | CENTER LOWER_WALLS PRINT WHOLEMOLECULES DISTANCE MATHEVAL CONSTANT BIASVALUE UPPER_WALLS METAD | bias function colvar generic vatom |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | FIXEDATOM PRINT TORSION MATHEVAL DISTANCE CENTER UPPER_WALLS METAD CUSTOM | bias function colvar generic vatom |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | UNITS PRINT ENDPLUMED POSITION ECV_MULTITHERMAL TORSION OPES_EXPANDED OPES_METAD ENERGY | setup colvar opes generic |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | PCAVARS LOWER_WALLS PRINT WHOLEMOLECULES UPPER_WALLS METAD | mapping bias generic |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | INCLUDE GROUP LOAD COMBINE PRINT PAIRENTROPY Q4 MATHEVAL CENTER Q6 METAD COORDINATIONNUMBER | generic bias function setup core gridtools vatom symfunc |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | RMSD COORDINATION LOWER_WALLS GROUP COMBINE UNITS PRINT BRIDGE FLUSH UPPER_WALLS WHOLEMOLECULES DISTANCE MATHEVAL ANGLE FIT_TO_TEMPLATE DISTANCES METAD | bias function setup colvar adjmat core generic multicolvar |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | HISTOGRAM INCLUDE GROUP CONVERT_TO_FES COMBINE PRINT DUMPGRID COM REWEIGHT_BIAS GYRATION DISTANCES METAD | bias function gridtools colvar core generic multicolvar vatom |
| 21.040 | A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms | bio | EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference | Faidon Brotzakis | GROUP PRINT COM WHOLEMOLECULES DISTANCE RESTART BIASVALUE EMMI MOLINFO UPPER_WALLS | bias setup colvar core generic vatom isdb |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | RMSD PRINT DISTANCE | generic colvar |
| 21.036 | Modelling the structure and interactions of intrinsically disordered peptides with multiple-replica, metadynamics-based sampling methods and force-field combinations | bio | Bias Exchange Metadynamics, PTWTE-metaD | Matteo Salvalaglio | DIHCOR ALPHARMSD COORDINATION LOWER_WALLS GROUP ANTIBETARMSD RANDOM_EXCHANGES PRINT PARABETARMSD GYRATION WHOLEMOLECULES UPPER_WALLS MOLINFO METAD ENERGY | generic bias colvar core secondarystructure multicolvar |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | PRINT UPPER_WALLS LOWER_WALLS DISTANCE | colvar bias generic |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | INCLUDE REWEIGHT_METAD UNITS PRINT ENERGY TORSION DISTANCE CONSTANT BIASVALUE METAD CUSTOM | bias function setup colvar generic |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | COORDINATION CONVERT_TO_FES FLUSH FIXEDATOM DISTANCE UPPER_WALLS METAD RMSD HISTOGRAM GROUP REWEIGHT_METAD PRINT DUMPGRID COM WHOLEMOLECULES POSITION MATHEVAL ENDPLUMED READ | bias function gridtools colvar core generic vatom |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | COORDINATION CONVERT_TO_FES UNITS UWALLS FLUSH OPT_AVERAGED_SGD ANGLES LOWER_WALLS LOAD BF_CHEBYSHEV DISTANCE RESTRAINT UPPER_WALLS METAD HISTOGRAM COMBINE REWEIGHT_METAD PRINT REWEIGHT_BIAS EXTERNAL COORDINATIONNUMBER DUMPGRID VES_LINEAR_EXPANSION DISTANCES TD_GRID | bias function setup gridtools colvar ves generic multicolvar symfunc |
| 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 | RESTART BF_LEGENDRE ECV_UMBRELLAS_LINE ECV_MULTITHERMAL_MULTIBARIC PRINT TD_UNIFORM VES_LINEAR_EXPANSION ENVIRONMENTSIMILARITY MATHEVAL VOLUME OPT_AVERAGED_SGD Q6 OPES_EXPANDED UPPER_WALLS ENERGY | envsim bias opes function setup colvar ves generic symfunc |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | GROUP PRINT COM WHOLEMOLECULES DISTANCE | colvar core vatom generic |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | COORDINATION PRINT WHOLEMOLECULES PBMETAD CENTER | generic vatom bias colvar |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | UNITS LOAD ENVIRONMENTSIMILARITY VOLUME MOLINFO OPES_EXPANDED UPPER_WALLS RMSD ECV_UMBRELLAS_LINE ECV_MULTITHERMAL_MULTIBARIC PRINT ENERGY ECV_LINEAR WHOLEMOLECULES ENDPLUMED POSITION MATHEVAL ECV_MULTITHERMAL TORSION Q6 CUSTOM | envsim bias opes function setup colvar generic symfunc |
| 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 UNITS PRINT DISTANCES METAD CUSTOM | bias function setup colvar generic multicolvar |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | COMBINE UNITS PRINT FLUSH UPPER_WALLS DISTANCE RESTART DISTANCES METAD | bias function setup colvar generic multicolvar |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | PRINT FLUSH UPPER_WALLS RESTART DISTANCES METAD PATH | bias mapping setup generic multicolvar |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | LOCAL_Q6 CONTACT_MATRIX MFILTER_MORE OUTPUT_CLUSTER CLUSTER_NATOMS FLUSH ENDPLUMED DFSCLUSTERING COMMITTOR Q6 CLUSTER_WITHSURFACE | adjmat generic clusters multicolvar symfunc |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | HISTOGRAM COORDINATION GROUP CONVERT_TO_FES REWEIGHT_METAD PRINT DUMPGRID COM FLUSH UPPER_WALLS WHOLEMOLECULES POSITION MATHEVAL ENDPLUMED READ FIT_TO_TEMPLATE WRAPAROUND METAD | bias function gridtools colvar core generic vatom |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | LOWER_WALLS PRINT TORSION DISTANCE COMMITTOR CENTER UPPER_WALLS METAD | colvar bias vatom generic |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | ALPHABETA INCLUDE COORDINATION GROUP CS2BACKBONE METAINFERENCE PRINT GYRATION WHOLEMOLECULES DISTANCE PBMETAD CENTER MOLINFO | bias colvar core generic multicolvar vatom isdb |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | INCLUDE LOWER_WALLS COMBINE RANDOM_EXCHANGES PRINT FLUSH UPPER_WALLS DISTANCE ANGLE DISTANCES MOLINFO METAD ERMSD | bias function colvar generic multicolvar |
| 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 LOWER_WALLS COM PRINT UPPER_WALLS METAD FUNNEL | vatom generic funnel bias |
| 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 BIASVALUE EMMIVOX PRINT GROUP MOLINFO | isdb generic core bias |
| 25.006 | Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations | methods | Enhanced sampling, Atomistic simulations, Conformational ensemble, PROTACs, Targeted Protein Degradation, Chamelonic molecules | Shikshya Bhusal, Omar Valsson | INCLUDE WHOLEMOLECULES READ PBMETAD ENERGY PRINT CENTER UPDATE_IF DISTANCE DUMPATOMS VOLUME TORSION GYRATION MOLINFO RESTART | generic vatom colvar bias setup |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | LOAD ENERGY COMBINE OPES_METAD PRINT DISTANCE CUSTOM COORDINATION GROUP TORSION | generic colvar core function setup opes |
| 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 | WHOLEMOLECULES LOWER_WALLS GROUP MATHEVAL ECV_MULTITHERMAL ENERGY OPES_METAD_EXPLORE PRINT CENTER OPES_EXPANDED DISTANCE ENDPLUMED COORDINATION FIXEDATOM UPPER_WALLS ANGLE TORSION FIT_TO_TEMPLATE | generic vatom colvar core bias function opes |
| 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 | ECV_MULTITHERMAL ENERGY COMBINE OPES_METAD_EXPLORE PRINT OPES_EXPANDED DISTANCE CUSTOM COORDINATION GROUP TORSION RESTART | generic colvar core function setup opes |
| 24.020 | Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics | bio | LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning | Ziyue Zou, Dedi Wang, Pratyush Tiwary | LOAD PRINT GROUP TORSION COMMITTOR METAD | generic colvar core bias setup |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | GROUP LOWER_WALLS MATHEVAL COORDINATIONNUMBER COM ENERGY OPES_METAD PRINT UNITS DISTANCE DISTANCES FIXEDATOM UPPER_WALLS ZDISTANCES FLUSH CUSTOM COMMITTOR | generic multicolvar vatom symfunc colvar core bias function setup opes |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | LOAD PBMETAD PRINT | generic bias setup |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | WHOLEMOLECULES COM COMBINE PRINT DISTANCE UPPER_WALLS FLUSH TORSION METAD | generic vatom colvar bias function |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | COM ALPHARMSD PRINT DISTANCE ANGLE DUMPFORCES CONTACTMAP METAD MOLINFO | generic vatom colvar bias secondarystructure |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | LOAD BIASVALUE COMBINE PRINT GHBFIX FLUSH COORDINATION CUSTOM UPPER_WALLS GROUP METAD MOLINFO | generic colvar core bias function setup |
| 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 | LOWER_WALLS MATHEVAL PRINT CELL CUSTOM UPPER_WALLS COMMITTOR METAD DRMSD | generic colvar bias function |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | WHOLEMOLECULES FUNNEL_PS LOWER_WALLS COM PRINT DISTANCE UPPER_WALLS PATHMSD METAD FUNNEL | generic vatom colvar funnel bias |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | BF_FOURIER OPT_AVERAGED_SGD TORSION PRINT VES_LINEAR_EXPANSION TD_UNIFORM | ves colvar generic |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | LOWER_WALLS MATHEVAL COM LOAD OPES_METAD_EXPLORE OPES_METAD PRINT UNITS PYTORCH_MODEL COORDINATION CUSTOM DISTANCE UPPER_WALLS GROUP | generic vatom colvar core bias function pytorch setup opes |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | INCLUDE CONSTANT COMBINE PRINT MOVINGRESTRAINT RESTRAINT UPPER_WALLS METAD | generic bias function |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | MATHEVAL OPES_METAD ENDPLUMED WHOLEMOLECULES LOAD PRINT UPPER_WALLS FIT_TO_TEMPLATE UNITS DISTANCES ANGLE GROUP TORSION LOWER_WALLS CENTER DISTANCE PYTORCH_MODEL COORDINATION FIXEDATOM | generic multicolvar vatom colvar core bias function pytorch setup opes |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | WHOLEMOLECULES PBMETAD ALPHABETA ALPHARMSD PRINT REWEIGHT_BIAS GROUP CONTACTMAP METAD MOLINFO RESTART | generic colvar core secondarystructure bias setup multicolvar |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | FUNNEL_PS LOWER_WALLS COM PRINT DISTANCE UPPER_WALLS METAD FUNNEL | generic vatom colvar funnel bias |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | WHOLEMOLECULES MATHEVAL PBMETAD CONSTANT BIASVALUE PRINT TORSION RESTART | generic colvar bias function setup |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | INCLUDE WHOLEMOLECULES SAXS STATS BIASVALUE PRINT CENTER DISTANCE RESTRAINT ENSEMBLE GROUP MOLINFO | generic vatom colvar core bias function isdb |
| 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 | WHOLEMOLECULES STATS PRINT RESTRAINT COORDINATION MOLINFO | generic colvar bias function |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | OPES_METAD PRINT EXTERNAL ENDPLUMED UNITS TORSION POSITION METAD | generic colvar bias setup opes |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | COM ENERGY PRINT DISTANCE UPPER_WALLS GYRATION METAD MOLINFO | vatom generic colvar bias |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | LOWER_WALLS COM PRINT CENTER DISTANCE UPPER_WALLS GROUP METAD RESTART | generic vatom colvar core bias setup |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | INPLANEDISTANCES COM PRINT MOVINGRESTRAINT DISTANCES FLUSH RESTART | generic vatom bias setup multicolvar |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | INCLUDE WHOLEMOLECULES GROUP MATHEVAL PBMETAD ALPHABETA SAXS STATS COMBINE BIASVALUE PRINT CENTER ENDPLUMED COORDINATION ENSEMBLE ANGLE MOLINFO | generic vatom colvar core bias function isdb multicolvar |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | CLUSTER_NATOMS OUTER_PRODUCT SMAC OUTPUT_CLUSTER COORDINATIONNUMBER Q6 LOCAL_Q6 CLUSTER_DISTRIBUTION PRINT METAD CLUSTER_PROPERTIES CUSTOM DISTANCES CONTACT_MATRIX DFSCLUSTERING ONES MORE_THAN MATRIX_VECTOR_PRODUCT | matrixtools generic symfunc bias function adjmat clusters multicolvar |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | WHOLEMOLECULES LOWER_WALLS GROUP PBMETAD ALPHABETA CS2BACKBONE BIASVALUE PRINT ANTIBETARMSD ENDPLUMED UPPER_WALLS FLUSH MOLINFO RESTART | generic core bias secondarystructure setup isdb multicolvar |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | ENERGY EXTERNAL COORDINATION GROUP METAD | colvar core bias |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | EDS COMBINE PRINT DISTANCE RESTRAINT TORSION | generic colvar bias function eds |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | WHOLEMOLECULES ENERGY ALPHARMSD PRINT ENDPLUMED GYRATION METAD MOLINFO | generic colvar bias secondarystructure |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | EMMI BIASVALUE PRINT GROUP MOLINFO | isdb generic core bias |
| 26.008 | Ensemble Dynamics | methods | State Exploration, Protein Folding, Drug Binding, Phase Transition | Florian M. Dietrich | LOAD CUSTOM BIASVALUE GROUP DISTANCE CELL OPES_METAD_EXPLORE UNITS POSITION TORSION PRINT | setup generic bias opes colvar core function |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | METAD COMBINE DISTANCE UNITS CENTER OPES_METAD CUSTOM BIASVALUE WHOLEMOLECULES COORDINATION ENERGY FIXEDATOM ENDPLUMED INCLUDE FIT_TO_TEMPLATE LOWER_WALLS RMSD GROUP OPES_METAD_EXPLORE POSITION MATHEVAL CONTACTMAP MOLINFO FLUSH PYTORCH_MODEL PRINT UPPER_WALLS | setup generic bias opes vatom colvar core pytorch function |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | DUMPMASSCHARGE MOLINFO METAD RESTRAINT COMBINE DISTANCE FIXEDATOM CENTER PRINT UPPER_WALLS | colvar bias vatom generic function |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | ALPHARMSD FIT_TO_TEMPLATE MOLINFO METAD COMBINE WHOLEMOLECULES POSITION ANN PRINT | colvar annfunc bias secondarystructure generic function |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | PATHMSD CUSTOM SKETCHMAP_PROJECTION METAD TRANSPOSE COLLECT_FRAMES COM DISTANCE WHOLEMOLECULES LANDMARK_SELECT_FPS DISSIMILARITIES VORONOI SKETCHMAP VSTACK PRINT UPPER_WALLS | dimred generic matrixtools valtools bias vatom colvar landmarks function |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | MOLINFO METAD DISTANCE ECV_MULTITHERMAL OPES_METAD_EXPLORE ENDPLUMED ENERGY TORSION OPES_EXPANDED PRINT | generic opes colvar bias |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | CONTACTMAP ECV_UMBRELLAS_LINE WHOLEMOLECULES ECV_MULTITHERMAL ENERGY OPES_EXPANDED PRINT | colvar generic opes |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | RESTART ALPHABETA ALPHARMSD MOLINFO ANTIBETARMSD COM WHOLEMOLECULES PBMETAD TORSION PRINT | setup colvar bias vatom multicolvar secondarystructure generic |
| 22.021 | Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn Løland Bore | LOWER_WALLS OPES_EXPANDED ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY INCLUDE PRINT UPPER_WALLS | generic opes envsim bias |
| 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 | WHOLEMOLECULES METAD PRINT LOAD | generic setup bias |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | MATHEVAL LOAD FIT_TO_TEMPLATE ANGLE FLUSH GROUP DISTANCE COMMITTOR WHOLEMOLECULES COORDINATION ENERGY FIXEDATOM ENDPLUMED CENTER PYTORCH_MODEL PRINT UPPER_WALLS | setup colvar bias vatom generic core pytorch function |
| 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 | STATS MOLINFO RESTRAINT COMBINE WHOLEMOLECULES COORDINATION PRINT | generic colvar function bias |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | LOAD LOWER_WALLS COMBINE GROUP DISTANCE DISTANCES ENERGY UNITS TORSION PRINT UPPER_WALLS | setup generic bias multicolvar colvar core function |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | TORSION METAD PRINT | colvar generic bias |
| 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 | MATHEVAL LOAD LOWER_WALLS CONTACTMAP BIASVALUE MOLINFO METAD CONSTANT GROUP FUNCPATHGENERAL COM PROJECTION_ON_AXIS WHOLEMOLECULES DISTANCE INCLUDE PRINT UPPER_WALLS | setup generic bias vatom colvar core function |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | MATHEVAL LOWER_WALLS MOLINFO METAD RMSD COMBINE DISTANCE WHOLEMOLECULES ENERGY CENTER PRINT UPPER_WALLS | colvar bias vatom generic function |
| 19.081 | Calculation of phase diagrams in the multithermal-multibaric ensemble | methods | VES, variationally enhanced sampling, multithermal-multibaric, energy, Wang Landau, RefCV, kernel, bcc, fcc, sodium, aluminum | Pablo Piaggi | RESTART COMBINE TD_WELLTEMPERED REWEIGHT_BIAS LOAD CELL ENERGY DUMPGRID OPT_DUMMY LOWER_WALLS VES_LINEAR_EXPANSION TD_MULTITHERMAL_MULTIBARIC OPT_AVERAGED_SGD REWEIGHT_TEMP_PRESS Q6 READ MATHEVAL BF_LEGENDRE VOLUME HISTOGRAM CONVERT_TO_FES PRINT UPPER_WALLS | symfunc setup generic gridtools bias ves colvar function |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | LOWER_WALLS ANGLE FLUSH COMBINE DUMPGRID BF_CHEBYSHEV VES_LINEAR_EXPANSION DISTANCE EXTERNAL CONVERT_TO_FES COORDINATION UNITS HISTOGRAM OPT_AVERAGED_SGD TD_WELLTEMPERED TD_GRID PRINT UPPER_WALLS | setup generic gridtools bias ves colvar function |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | MOLINFO METAD RMSD ERMSD DISTANCE WHOLEMOLECULES TORSION PRINT | generic colvar bias |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | GROUP DISTANCE ENDPLUMED CENTER INCLUDE PRINT | colvar generic core vatom |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | RESTART DISTANCE_FROM_CONTOUR METAD UPPER_WALLS COMBINE HISTOGRAM CONVERT_TO_FES DUMPGRID REWEIGHT_BIAS PRINT READ | setup gridtools contour bias generic function |
| 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 | RESTART LOWER_WALLS FLUSH METAD GROUP COORDINATION POSITION UNITS PRINT UPPER_WALLS | setup colvar bias generic core |
| 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 | METAD COM DISTANCE ENERGY PRINT UPPER_WALLS | vatom generic colvar bias |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | MOLINFO RMSD METAD ERMSD WHOLEMOLECULES ENDPLUMED PRINT | generic colvar bias |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | RESTART VES_DELTA_F LOAD METAD ENDPLUMED ENERGY TORSION POSITION UNITS PRINT | setup colvar bias ves generic |
| 26.006 | Metadynamics simulations of buried phosphorylation sites and proline isomerisation | bio | metadynamics | Julian Streit | METAD PRINT TORSION COORDINATION MOLINFO WHOLEMOLECULES | colvar generic bias |
| 25.029 | Energetic Constraints in the Enzymatic Depolymerization of Crystalline PET from enhanced molecular simulations | bio | HREX-Metadynamics, PETase, crystalline PET, amorphous PET, conformational ensembles, substrate binding, chain detachment | Ania Di Pede-Mattatelli and Francesco Colizzi | METAD DUMPGRID LOWER_WALLS REWEIGHT_BIAS PRINT CONVERT_TO_FES HISTOGRAM UPPER_WALLS MOLINFO COM DISTANCE FIXEDATOM WHOLEMOLECULES | gridtools generic vatom colvar bias |
| 25.023 | Molecular simulations of Tau-protein oligomers | bio | metadynamics, proteins, aggregation | Giovanni Bussi | METAD DUMPGRID RESTART PRINT CONVERT_TO_FES REWEIGHT_BIAS RMSD HISTOGRAM FLUSH RESTRAINT CONTACTMAP CUSTOM | gridtools generic setup colvar bias function |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | SAXS WHOLEMOLECULES GYRATION PRINT TORSION STATS UPPER_WALLS FLUSH CENTER ENSEMBLE MOLINFO DISTANCE METAINFERENCE PBMETAD | generic vatom colvar isdb bias function |
| 25.014 | Atomic resolution ensembles of intrinsically disordered proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | BAIES GROUP BIASVALUE PRINT | generic core isdb bias |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | PRINT GROUP FLUSH ABMD COM COMMITTOR DISTANCE WHOLEMOLECULES | core generic vatom colvar bias |
| 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 | UNITS ZDISTANCES PRINT COORDINATIONNUMBER GROUP OPES_METAD UPPER_WALLS FLUSH COMMITTOR DISTANCE FIXEDATOM DISTANCES CUSTOM | generic setup symfunc core vatom colvar multicolvar opes bias function |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | WHOLEMOLECULES PRINT ENERGY OPES_METAD COMBINE GROUP TORSION MATHEVAL PYTORCH_MODEL MOLINFO COMMITTOR DISTANCE ENDPLUMED CUSTOM | generic core colvar pytorch opes function |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | PRINT ERMSD GROUP BIASVALUE INCLUDE EMMIVOX MOLINFO RESTRAINT WHOLEMOLECULES | core generic colvar isdb bias |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | UNITS METAD PRINT GROUP TORSION | generic core setup colvar bias |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | UNITS METAD RESTART PRINT TORSION | generic colvar setup bias |
| 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 | METAD PRINT RMSD MATHEVAL MOLINFO DISTANCE WHOLEMOLECULES | colvar generic bias function |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | METAD PRINT COORDINATIONNUMBER GROUP INCLUDE LOAD CENTER | setup symfunc generic core vatom bias |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | UNITS LOCAL_Q3 DUMPGRID DFSCLUSTERING CLUSTER_DISTRIBUTION LOCAL_AVERAGE PRINT Q3 GROUP HISTOGRAM COORDINATIONNUMBER CLUSTER_NATOMS LOAD DENSITY AROUND RESTRAINT FIXEDATOM CONTACT_MATRIX | gridtools setup symfunc generic core vatom adjmat clusters bias volumes |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | GYRATION PRINT COORDINATION UPPER_WALLS COM DISTANCE PBMETAD | colvar generic bias vatom |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | UNITS LOWER_WALLS PRINT POSITION OPES_METAD BIASVALUE UPPER_WALLS PYTORCH_MODEL ENDPLUMED CUSTOM | generic setup colvar pytorch opes bias function |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | MFILTER_MORE DFSCLUSTERING LOCAL_Q6 PRINT LOCAL_AVERAGE COORDINATIONNUMBER GROUP COMBINE MFILTER_LESS Q6 CLUSTER_NATOMS Q4 LOCAL_Q4 CONTACT_MATRIX | generic symfunc core adjmat multicolvar clusters function |
| 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 | GYRATION TORSION MOLINFO WHOLEMOLECULES PBMETAD | colvar generic bias |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | UNITS DUMPGRID PRINT CONVERT_TO_FES COORDINATIONNUMBER HISTOGRAM CUSTOM BIASVALUE LOAD UPPER_WALLS FLUSH VOLUME MOVINGRESTRAINT RESTRAINT ANN COMMITTOR REWEIGHT_BIAS | annfunc gridtools generic setup symfunc colvar bias function |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | PRINT GROUP BIASVALUE LOAD EMMIVOX MOLINFO WHOLEMOLECULES | setup core generic isdb 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 | UNITS METAD GYRATION LOWER_WALLS COMBINE COORDINATIONNUMBER COORDINATION UPPER_WALLS FLUSH COM DISTANCE | symfunc setup generic vatom colvar bias function |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | UNITS METAD LOWER_WALLS PRINT UPPER_WALLS COM DISTANCE WHOLEMOLECULES | generic setup vatom colvar bias |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | PRINT MATHEVAL TORSIONS COM DISTANCE KDE | gridtools generic vatom colvar multicolvar function |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | SAXS WHOLEMOLECULES GYRATION PRINT GROUP EEFSOLV BIASVALUE FLUSH CENTER MOLINFO ALPHARMSD METAINFERENCE PBMETAD | generic core vatom secondarystructure colvar isdb bias |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | METAD RANDOM_EXCHANGES PUCKERING LOWER_WALLS DUMPGRID PRINT ENERGY GROUP REWEIGHT_METAD HISTOGRAM COORDINATION UPPER_WALLS INCLUDE MOLINFO DISTANCE WHOLEMOLECULES | gridtools generic core colvar bias |
| 20.027 | Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery | bio | SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery | Khaled Abdel-Maksoud | METAD DISTANCE TORSION PRINT | colvar generic bias |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | FIT_TO_TEMPLATE WHOLEMOLECULES PRINT ENERGY GROUP OPES_METAD MATHEVAL COORDINATION PYTORCH_MODEL UPPER_WALLS ANGLE CENTER DISTANCE FIXEDATOM ENDPLUMED | core generic vatom colvar pytorch opes bias function |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | METAD LOWER_WALLS PRINT ENERGY MATHEVAL UPPER_WALLS VOLUME CELL | colvar generic bias function |
| 20.014 | amyloid beta small molecule interaction | bio | intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta | Gabriella Heller | DIHCOR ANTIBETARMSD TORSION STATS GYRATION COORDINATION ALPHARMSD PARABETARMSD WHOLEMOLECULES PBMETAD CS2BACKBONE PRINT GROUP MOLINFO ENDPLUMED METAINFERENCE COMBINE INCLUDE FLUSH ENSEMBLE | generic core secondarystructure colvar isdb multicolvar bias function |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | METAD RESTART PRINT COMBINE RMSD TORSION UPPER_WALLS MOLINFO DISTANCE WHOLEMOLECULES | generic setup colvar bias function |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | UNITS METAD RESTART PRINT COORDINATIONNUMBER GROUP COMBINE UPPER_WALLS FLUSH ENDPLUMED DISTANCES | generic symfunc setup core multicolvar bias function |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | UNITS METAD RESTART PRINT COORDINATIONNUMBER GROUP COMBINE FLUSH EXTERNAL ENDPLUMED | generic symfunc setup core bias function |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | UNITS MAZE_LOSS PRINT POSITION MAZE_SIMULATED_ANNEALING MAZE_OPTIMIZER_BIAS | generic colvar maze setup |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | PATHMSD METAD LOWER_WALLS PRINT UPPER_WALLS WHOLEMOLECULES | colvar generic bias |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | UNITS PRINT ENERGY POSITION Q6 TORSION LOAD ENDPLUMED ENVIRONMENTSIMILARITY | generic setup symfunc colvar envsim |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | METAD PRINT FUNCPATHMSD RMSD CONTACTMAP COM DISTANCE ENDPLUMED WHOLEMOLECULES | generic vatom colvar bias function |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | METAD GYRATION LOWER_WALLS ALPHABETA PRINT GROUP UPPER_WALLS MOLINFO WHOLEMOLECULES | core generic colvar multicolvar bias |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | METAD LOWER_WALLS PRINT ENERGY COMBINE TORSION MATHEVAL UPPER_WALLS VOLUME CELL ENDPLUMED | colvar generic bias function |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | METAD GYRATION RESTART PRINT COORDINATIONNUMBER ENDPLUMED DISTANCES | generic symfunc setup colvar multicolvar bias |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | PUCKERING TORSION BIASVALUE MATHEVAL INCLUDE MOLINFO CONSTANT | colvar generic bias function |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | SAXS PRINT GROUP RMSD BIASVALUE INCLUDE UPPER_WALLS STATS CENTER MOLINFO RESTRAINT DISTANCE ENDPLUMED WHOLEMOLECULES | generic core vatom colvar isdb bias function |
| 26.012 | Buprenorphine Restricts the Conformational Landscape of the μ-Opioid Receptor | bio | OneOPES, GPCR, MOR, activation, euclidean path, conformational changes, allostery | Simone Aureli | ENERGY PATH OPES_METAD_EXPLORE OPES_EXPANDED PRINT GROUP VOLUME RMSD ECV_MULTITHERMAL CUSTOM UPPER_WALLS CENTER COORDINATION DISTANCE | generic function opes bias core vatom colvar mapping |
| 26.000 | OPES simulations of disordered proteins | bio | OPES, IDPs | Julian Streit | RESTART ENERGY OPES_EXPANDED PRINT ECV_MULTITHERMAL | setup colvar opes generic |
| 25.022 | Imidazole Diffusion in SALEM-2 MOF | materials | OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials | Sudheesh Kumar Ethirajan | UNITS PROJECTION_ON_AXIS WHOLEMOLECULES PRINT GROUP MOLINFO DISTANCES OPES_METAD ENDPLUMED CENTER DISTANCE | generic multicolvar opes vatom core setup colvar |
| 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 | ENERGY OPES_METAD_EXPLORE PATHMSD PRINT OPES_EXPANDED GROUP RMSD DISTANCES LOWER_WALLS ECV_MULTITHERMAL CUSTOM UPPER_WALLS CENTER COORDINATION GHOST DISTANCE | generic multicolvar function opes bias core vatom colvar |
| 24.025 | Correlating Enzymatic Reactivity for Different Substrates using Transferable Data-Driven Collective Variables | bio | enzymatic reactivity, k_cat, transfer learning, data-driven CVs, catalysis, ligand-binding modes, water, alpha-amylase, sugar, classical MD, OPES, machine learning, Deep TDA CV, path CV | Sudip Das | RESTART FIT_TO_TEMPLATE WHOLEMOLECULES FIXEDATOM PATH PRINT GROUP TORSION LOWER_WALLS OPES_METAD CUSTOM UPPER_WALLS CENTER COORDINATION PYTORCH_MODEL DISTANCE | generic pytorch function vatom bias core opes setup colvar mapping |
| 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 |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | UNITS WHOLEMOLECULES PRINT COMBINE METAD DISTANCE | generic function bias setup colvar |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | CENTER UNITS COM POSITION WHOLEMOLECULES PRINT GROUP DISTANCES CUSTOM METAD FLUSH DISTANCE | generic multicolvar function vatom bias core setup colvar |
| 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 | GROUP TORSION DISTANCE UNITS FIT_TO_TEMPLATE POSITION OPES_METAD_EXPLORE PRINT WRAPAROUND CUSTOM BIASVALUE COM WHOLEMOLECULES LOWER_WALLS UPPER_WALLS CENTER COORDINATION ENERGY COMMITTOR MOLINFO OPES_METAD ENDPLUMED MATHEVAL FLUSH | generic function opes bias core vatom setup colvar |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | MFILTER_MORE COORDINATIONNUMBER PRINT MOVINGRESTRAINT GROUP LOCAL_Q6 COMBINE LOWER_WALLS METAD Q6 | generic multicolvar function symfunc bias core |
| 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 | UNITS FIT_TO_TEMPLATE WHOLEMOLECULES FIXEDATOM PATH OPES_METAD_EXPLORE PRINT GROUP TORSION LOWER_WALLS OPES_METAD CUSTOM UPPER_WALLS CENTER COORDINATION PYTORCH_MODEL DISTANCE | generic pytorch function vatom opes core bias setup colvar mapping |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | UNITS ENERGY PIV PRINT LOCAL_AVERAGE VOLUME PAIRENTROPY CUSTOM UPPER_WALLS METAD Q6 FUNCPATHMSD Q4 RESTRAINT | generic gridtools function symfunc bias piv setup colvar |
| 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 | ENERGY WHOLEMOLECULES PRINT LOWER_WALLS UPPER_WALLS CONTACTMAP METAD | generic colvar bias |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | UNITS OPES_METAD_EXPLORE PRINT CUSTOM COORDINATION PYTORCH_MODEL | generic pytorch function opes setup colvar |
| 22.032 | Reciprocal barrier restraint. Application to path-meta-eABF | methods | restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC | Istvan Kolossvary | METAD PATHMSD PRINT CUSTOM DRR FLUSH BIASVALUE | generic drr function bias colvar |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | CONSTANT GROUP TORSION DISTANCE UNITS POSITION PRINT COMBINE CUSTOM BIASVALUE PYTORCH_MODEL WHOLEMOLECULES INCLUDE CONTACTMAP ENERGY COMMITTOR MOLINFO OPES_METAD ENDPLUMED RMSD | generic pytorch function bias opes core setup colvar |
| 22.023 | Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy | bio | CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble | Faidon Brotzakis | RESTART COM WHOLEMOLECULES PRINT GROUP RMSD MOLINFO TORSION EMMI UPPER_WALLS COORDINATION BIASVALUE PBMETAD | generic isdb vatom bias core setup 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 |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | ENERGY WHOLEMOLECULES PRINT MATHEVAL INCLUDE MOLINFO LOWER_WALLS ALPHARMSD UPPER_WALLS CONTACTMAP METAD DISTANCE | generic function secondarystructure bias colvar |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | UNITS COM WHOLEMOLECULES PATHMSD PRINT UPPER_WALLS METAD DISTANCE | generic bias vatom setup colvar |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | COM ENERGY PRINT MOLINFO LOWER_WALLS UPPER_WALLS GYRATION PBMETAD DISTANCE | generic bias colvar vatom |
| 20.034 | Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations | bio | RNA, SARS-CoV-2, partial tempering | Sandro Bottaro | RESTART ABMD ERMSD PRINT MOLINFO TORSION CENTER DISTANCE | generic vatom bias setup colvar |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | WHOLEMOLECULES READ PRINT DUMPGRID HISTOGRAM GROUP MOLINFO DISTANCES EMMI BIASVALUE RMSD CONVERT_TO_FES | generic isdb gridtools multicolvar bias core colvar |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | TORSION PRINT ENDPLUMED | generic colvar |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | RESTART FIT_TO_TEMPLATE PRINT METAD CENTER DISTANCE | generic vatom bias setup colvar |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | LOAD PRINT VOLUME GROUP INCLUDE UPPER_WALLS METAD CENTER | generic bias vatom core setup colvar |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | UNITS PRINT MOVINGRESTRAINT ENDPLUMED GYRATION | setup colvar bias generic |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | DUMPDERIVATIVES ANGLE PRINT GROUP DISTANCE TORSION COMBINE CUSTOM ENDPLUMED CENTER RESTRAINT | generic function vatom bias core colvar |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | WHOLEMOLECULES RESTRAINT LOWER_WALLS ENDPLUMED COORDINATION DISTANCE | generic colvar bias |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | COM ANN POSITION COMBINE RESTRAINT | function bias vatom annfunc colvar |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | UNITS ENERGY PRINT LOWER_WALLS COMBINE UPPER_WALLS METAD FLUSH DISTANCE | generic function bias setup colvar |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | COM WHOLEMOLECULES CONSTANT PRINT MATHEVAL LOWER_WALLS UPPER_WALLS METAD BIASVALUE DISTANCE | generic function bias vatom colvar |
| 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 | COM ALPHABETA WHOLEMOLECULES PRINT BRIDGE GROUP REWEIGHT_METAD MOLINFO TORSION LOWER_WALLS DISTANCES COMBINE FUNNEL UPPER_WALLS METAD RMSD DISTANCE | generic funnel multicolvar function adjmat vatom bias core colvar |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | COM WHOLEMOLECULES PRINT LOWER_WALLS FUNNEL UPPER_WALLS FUNNEL_PS METAD RMSD DISTANCE | generic funnel bias vatom colvar |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | WHOLEMOLECULES CS2BACKBONE PRINT JCOUPLING STATS METAINFERENCE MOLINFO TORSION ENSEMBLE ENDPLUMED GYRATION FLUSH PBMETAD BIASVALUE RDC | generic isdb function bias colvar |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | TORSION PRINT DRR | generic colvar drr |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | ALPHABETA PRINT COMMITTOR MOLINFO COMBINE METAD FLUSH | multicolvar bias function generic |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | WHOLEMOLECULES CS2BACKBONE PRINT GROUP METAINFERENCE MOLINFO RDC | generic isdb core |