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 |
|---|---|---|---|---|---|---|
| 26.002 | 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 | DISTANCE OPES_EXPANDED ECV_MULTITHERMAL PATH CUSTOM OPES_METAD_EXPLORE GROUP COORDINATION ENERGY VOLUME RMSD PRINT LOWER_WALLS CENTER UPPER_WALLS PATHMSD | bias opes colvar generic vatom function core mapping |
| 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 | EMMIVOX GROUP WHOLEMOLECULES MOLINFO PRINT BIASVALUE | bias core generic isdb |
| 25.015 | Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY | materials | Molecular crystal, Force Field, Collective Variable | Pradip Si and Omar Valsson | DISTANCES SMAC DUMPMULTICOLVAR TORSIONS PRINT | multicolvar generic symfunc |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | DISTANCE GYRATION PYTORCH_MODEL RESTRAINT PRINT | bias generic colvar pytorch |
| 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 | DISTANCE OPES_METAD DISTANCES CUSTOM ZDISTANCES COORDINATIONNUMBER UNITS GROUP FIXEDATOM COMMITTOR PRINT FLUSH UPPER_WALLS | bias opes colvar generic vatom multicolvar function symfunc core setup |
| 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 | DISTANCE DUMPATOMS EMMI PARABETARMSD ALPHARMSD CENTER GROUP COORDINATION PBMETAD WHOLEMOLECULES COM RMSD MOLINFO PRINT BIASVALUE DUMPMASSCHARGE UPPER_WALLS | bias generic colvar isdb vatom secondarystructure core |
| 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 | DISTANCE TORSION ECV_MULTITHERMAL CUSTOM OPES_METAD_EXPLORE GROUP COORDINATION ENERGY RESTART PRINT OPES_EXPANDED COMBINE | opes colvar generic function core setup |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | DISTANCE DUMPATOMS DISTANCES UNITS GROUP POSITION FIT_TO_TEMPLATE MATHEVAL WRAPAROUND RESTART COM LOWER_WALLS PRINT METAD FLUSH WHOLEMOLECULES UPPER_WALLS | bias generic colvar vatom multicolvar function core setup |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | PBMETAD PINES PRINT LOAD | bias pines generic setup |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | OPES_METAD CUSTOM PYTORCH_MODEL UNITS POSITION ENDPLUMED PRINT LOWER_WALLS BIASVALUE UPPER_WALLS | bias opes colvar setup generic function pytorch |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | DISTANCE TORSION CUSTOM FIXEDATOM MATHEVAL PRINT METAD CENTER UPPER_WALLS | bias generic colvar vatom function |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | DISTANCE MATHEVAL PBMETAD WHOLEMOLECULES CONSTANT PRINT BIASVALUE ANGLE | bias generic function colvar |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | TORSION DISTANCE ECV_MULTITHERMAL OPES_METAD_EXPLORE ENDPLUMED ENERGY MOLINFO PRINT METAD OPES_EXPANDED | generic opes colvar bias |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | DISTANCE METAD PRINT DISTANCES | bias generic colvar multicolvar |
| 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 | DISTANCE TORSION GROUP COM PRINT METAD WHOLEMOLECULES | bias generic colvar vatom core |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | CLUSTER_NATOMS HISTOGRAM MFILTER_MORE DFSCLUSTERING CLUSTER_DISTRIBUTION DUMPGRID FIXEDATOM COORDINATIONNUMBER GROUP CONTACT_MATRIX PRINT METAD Q6 LOCAL_Q6 INSPHERE COMBINE | gridtools bias generic clusters vatom multicolvar function symfunc volumes core adjmat |
| 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 | TORSION RANDOM_EXCHANGES ENDPLUMED PBMETAD PRINT METAD INCLUDE | generic colvar bias |
| 20.034 | Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations | bio | RNA, SARS-CoV-2, partial tempering | Sandro Bottaro | DISTANCE TORSION ABMD RESTART ERMSD MOLINFO PRINT CENTER | bias generic colvar vatom setup |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | GROUP VOLUME INCLUDE PRINT LOAD METAD CENTER UPPER_WALLS | bias generic colvar vatom core setup |
| 20.002 | Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study | bio | Metadynamics, path CVs | Riccardo Ocello | GROUP RESTART MOLINFO PRINT METAD WHOLEMOLECULES UPPER_WALLS PATHMSD | bias generic colvar core setup |
| 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 | CS2BACKBONE ENDPLUMED GROUP ANTIBETARMSD PBMETAD ALPHABETA WHOLEMOLECULES MOLINFO PRINT LOWER_WALLS FLUSH BIASVALUE UPPER_WALLS | bias generic isdb secondarystructure multicolvar core |
| 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 | DUMPGRID OPT_DUMMY Q6 CONVERT_TO_FES TD_WELLTEMPERED TD_MULTITHERMAL_MULTIBARIC VOLUME RESTART MATHEVAL ENERGY OPT_AVERAGED_SGD PRINT LOAD COMBINE REWEIGHT_BIAS HISTOGRAM BF_LEGENDRE VES_LINEAR_EXPANSION READ REWEIGHT_TEMP_PRESS LOWER_WALLS UPPER_WALLS CELL | gridtools bias colvar generic function symfunc setup ves |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | DISTANCE ENDPLUMED COORDINATION RESTRAINT LOWER_WALLS WHOLEMOLECULES | generic colvar bias |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | DISTANCE TORSION REWEIGHT_BIAS REWEIGHT_METAD EXTERNAL HISTOGRAM DUMPGRID MATHEVAL COMMITTOR PRINT METAD READ BIASVALUE CONVERT_TO_FES | bias gridtools generic colvar function |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | REWEIGHT_BIAS HISTOGRAM DUMPGRID UPPER_WALLS RESTART PRINT METAD READ CONVERT_TO_FES COMBINE DISTANCE_FROM_CONTOUR | bias gridtools contour generic function setup |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | DISTANCE TORSION EXTERNAL RESTART COMMITTOR COM ALPHABETA PRINT WHOLEMOLECULES COMBINE | bias generic colvar vatom multicolvar function setup |
| 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 | ANGLE METAD WHOLEMOLECULES PRINT DISTANCE | colvar generic bias |
| 25.022 | Imidazole Diffusion in SALEM-2 MOF | materials | OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials | Sudheesh Kumar Ethirajan | CENTER PROJECTION_ON_AXIS WHOLEMOLECULES PRINT ENDPLUMED MOLINFO DISTANCE GROUP UNITS DISTANCES OPES_METAD | colvar opes core vatom generic setup multicolvar |
| 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 | CENTER ENERGY ECV_MULTITHERMAL PRINT RMSD CUSTOM COMBINE MOLINFO DISTANCE COORDINATION OPES_EXPANDED GROUP GHOST OPES_METAD_EXPLORE | colvar opes core vatom generic function |
| 25.016 | Advancing in silico drug design with Bayesian refinement of AlphaFold models | bio | bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment | Samiran Sen | GROUP PRINT BAIES BIASVALUE | generic bias isdb core |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | METAD RESTART HISTOGRAM PRINT GROUP CUSTOM REWEIGHT_METAD READ DUMPGRID DISTANCE FLUSH UPPER_WALLS COORDINATION | colvar core generic function gridtools bias setup |
| 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 | CONVERT_TO_FES ANGLE WHOLEMOLECULES TORSION HISTOGRAM PRINT DISTANCE DUMPGRID GROUP COORDINATION | colvar core generic gridtools |
| 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 | CENTER ENERGY ANGLE ECV_MULTITHERMAL WHOLEMOLECULES TORSION PRINT ENDPLUMED LOWER_WALLS DISTANCE MATHEVAL FIXEDATOM FIT_TO_TEMPLATE GROUP COORDINATION OPES_METAD_EXPLORE UPPER_WALLS OPES_EXPANDED | colvar opes core vatom generic function bias |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | ENERGY RESTART INCLUDE TORSION BIASVALUE WHOLEMOLECULES PRINT MATHEVAL COORDINATION OPES_METAD_EXPLORE COM RMSD CONTACTMAP MOLINFO UPPER_WALLS GROUP PROJECTION_ON_AXIS ECV_MULTITHERMAL METAD CUSTOM LOWER_WALLS CONSTANT OPES_EXPANDED WRAPAROUND | colvar opes core vatom generic function bias setup |
| 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 | ENERGY RESTRAINT METAD RESTART TORSION PRINT COMMITTOR MATHEVAL DISTANCE FLUSH BIASVALUE MOLINFO COORDINATIONNUMBER | colvar generic function bias setup symfunc |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | ENERGY INCLUDE TORSION ENDPLUMED BIASVALUE CELL UNITS WHOLEMOLECULES PRINT POSITION DISTANCE MATHEVAL RMSD MOLINFO UPPER_WALLS GROUP CUSTOM LOAD LOWER_WALLS COORDINATION | colvar core generic function bias setup |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | METAD INCLUDE RESTART PRINT LOAD GROUP | generic bias setup core |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | COM PRINT LOWER_WALLS MOLINFO DISTANCE UPPER_WALLS PBMETAD GYRATION | vatom generic bias colvar |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | CENTER COM METAD WHOLEMOLECULES PRINT CUSTOM LOWER_WALLS DISTANCE UPPER_WALLS GROUP COORDINATION OPES_METAD_EXPLORE | colvar opes core vatom generic function 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 | CONVERT_TO_FES METAD WHOLEMOLECULES HISTOGRAM PRINT RMSD MATHEVAL MOLINFO DISTANCE REWEIGHT_METAD READ DUMPGRID | colvar generic function gridtools bias |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | TORSION PRINT METAD | colvar generic bias |
| 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 | COM METAD TORSION PRINT CUSTOM LOWER_WALLS DISTANCE UPPER_WALLS UNITS | colvar vatom generic function bias setup |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | ENERGY INCLUDE TORSION ENDPLUMED VOLUME Q6 UNITS WHOLEMOLECULES PRINT COMBINE DISTANCE FLUSH RMSD CONTACTMAP MOLINFO GROUP OPES_METAD PYTORCH_MODEL ECV_MULTITHERMAL LOAD ENVIRONMENTSIMILARITY OPES_EXPANDED | colvar opes core envsim generic function pytorch setup symfunc |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | DISTANCE RMSD PRINT | colvar generic |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | BIASVALUE UNITS OPT_AVERAGED_SGD HISTOGRAM PRINT COMBINE TD_WELLTEMPERED DISTANCE FLUSH REWEIGHT_METAD RESTRAINT BF_CHEBYSHEV UPPER_WALLS COORDINATIONNUMBER VES_LINEAR_EXPANSION OPES_METAD MOVINGRESTRAINT CONVERT_TO_FES METAD CUSTOM REWEIGHT_BIAS LOAD ANN CONSTANT DUMPGRID | colvar opes ves generic function gridtools annfunc bias setup symfunc |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | CENTER RESTRAINT INCLUDE SAXS WHOLEMOLECULES PRINT ENSEMBLE MOLINFO DISTANCE BIASVALUE GROUP STATS | colvar isdb core vatom generic function bias |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | ENERGY METAD PRINT VOLUME LOWER_WALLS MATHEVAL UPPER_WALLS CELL | function colvar generic bias |
| 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 | METAD PRINT CUSTOM COORDINATION DISTANCES UNITS | colvar generic function bias setup multicolvar |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | COM METAD INCLUDE TORSION WHOLEMOLECULES PRINT SORT MOLINFO DISTANCE MATHEVAL FLUSH COORDINATION MAXENT | colvar vatom generic function bias |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | FUNCPATHMSD METAD PRINT LOWER_WALLS UPPER_WALLS CELL PIV | colvar generic function piv bias |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | METAINFERENCE WHOLEMOLECULES TORSION RDC PRINT JCOUPLING CS2BACKBONE ENSEMBLE ENDPLUMED MOLINFO FLUSH BIASVALUE PBMETAD GYRATION STATS | colvar isdb generic function bias |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | ANGLE METAD INCLUDE PRINT COMBINE ERMSD LOWER_WALLS RANDOM_EXCHANGES MOLINFO FLUSH DISTANCE UPPER_WALLS DISTANCES | colvar generic function bias multicolvar |
| 26.009 | Exploring the Conformational Landscape of HIV-1 TAR RNA by PT-WTE | bio | RNA, PT-WTE, HIV-1 TAR | Stefano Bosio | MOLINFO PRINT METAD ENERGY GROUP WHOLEMOLECULES | colvar core bias generic |
| 26.006 | Metadynamics simulations of buried phosphorylation sites and proline isomerisation | bio | metadynamics | Julian Streit | MOLINFO PRINT METAD COORDINATION TORSION WHOLEMOLECULES | colvar bias generic |
| 25.024 | Sampling glycan-glycan interactions for B22 calculations | bio | B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange | Isabell Louise Grothaus | COM PRINT METAD POSITION COMBINE RESTRAINT DISTANCE | colvar bias vatom function generic |
| 24.001 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | bio | OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis | Dhiman Ray | PRINT CUSTOM COMMITTOR LOWER_WALLS OPES_METAD COMBINE TORSION UPPER_WALLS DISTANCE UNITS FLUSH | opes colvar bias setup function generic |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | DISTANCES COM PRINT POSITION CUSTOM METAD CENTER DISTANCE FLUSH GROUP WHOLEMOLECULES UNITS | colvar core bias multicolvar vatom setup function generic |
| 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 | MOLINFO PRINT RMSD METAD MATHEVAL DISTANCE WHOLEMOLECULES | colvar bias function generic |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | SKETCHMAP_PROJECTION COM VSTACK PRINT PATHMSD METAD CUSTOM TRANSPOSE LANDMARK_SELECT_FPS COLLECT_FRAMES VORONOI DISSIMILARITIES UPPER_WALLS DISTANCE SKETCHMAP WHOLEMOLECULES | colvar valtools matrixtools bias vatom landmarks dimred function generic |
| 23.016 | Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action | bio | G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics | Timothy Clark | READ MOLINFO PRINT RMSD METAD DUMPGRID MATHEVAL REWEIGHT_METAD DISTANCE HISTOGRAM CONVERT_TO_FES WHOLEMOLECULES | colvar gridtools bias function generic |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | PRINT DRR PATHMSD METAD CUSTOM BIASVALUE UPPER_WALLS LOWER_WALLS FLUSH | colvar bias drr function generic |
| 23.009 | Deep Learning Collective Variables from Transition Path Ensemble | methods | TPI-Deep-TDA, Deep-TDA, Transition Path, OPES, OPES Flooding, Machine Learning, Protein folding, Ligand binding | Dhiman Ray | ANGLE MOLINFO CUSTOM COMMITTOR ENDPLUMED COORDINATION OPES_METAD PRINT MATHEVAL COMBINE FIT_TO_TEMPLATE LOWER_WALLS GROUP PYTORCH_MODEL FIXEDATOM CENTER ENERGY CONTACTMAP RMSD INCLUDE DISTANCE UPPER_WALLS WHOLEMOLECULES | colvar opes pytorch core bias vatom function generic |
| 23.003 | Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations | methods | metadynamics, alchemical variable, alchemical free energy calculations | Wei-Tse Hsu | READ EXTRACV PRINT METAD TORSION | colvar bias generic |
| 22.017 | Water regulates the residence time of Benzamidine in Trypsin | bio | ligand binding, water, opes, benzamidine trypsin, unbinding rates, machine learning, Deep-LDA, Deep-TICA | Narjes Ansari | PYTORCH_MODEL PRINT FIXEDATOM CUSTOM WHOLEMOLECULES COMMITTOR COORDINATION MATHEVAL OPES_METAD CENTER FIT_TO_TEMPLATE LOWER_WALLS DISTANCE UPPER_WALLS GROUP RMSD | colvar opes pytorch core bias vatom function generic |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | TD_UNIFORM PRINT VES_LINEAR_EXPANSION BF_FOURIER OPT_AVERAGED_SGD TORSION | generic colvar ves |
| 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 DISTANCE PRINT | colvar generic vatom |
| 22.011 | Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck | methods | metadynamics, membrane permeation, protein folding | Shams Mehdi | XANGLES MOLINFO COM PRINT METAD CUSTOM ALPHABETA YANGLES COMBINE MATHEVAL TORSION UPPER_WALLS LOWER_WALLS DISTANCE WHOLEMOLECULES ZANGLES | colvar bias multicolvar vatom function generic |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | DISTANCES COM PRINT METAD DUMPGRID COMBINE INCLUDE GYRATION HISTOGRAM CONVERT_TO_FES GROUP REWEIGHT_BIAS | colvar function core bias multicolvar vatom gridtools generic |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | CENTER DISTANCE PRINT | colvar generic vatom |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | BF_LEGENDRE PRINT VES_LINEAR_EXPANSION METAD VOLUME TD_WELLTEMPERED PAIRENTROPY LOAD OPT_AVERAGED_SGD COMBINE ENERGY RESTART | colvar function ves bias setup gridtools generic |
| 21.030 | Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains | bio | parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure | Jim Pfaendtner | COM PRINT ALPHABETA METAD COORDINATION INCLUDE GYRATION TORSION DISTANCE PBMETAD ENERGY | colvar bias multicolvar vatom generic |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | MOLINFO PRINT EXTERNAL TORSION ENERGY FLUSH RESTART | colvar bias setup generic |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | COM PRINT PATHMSD METAD DISTANCE UPPER_WALLS UNITS WHOLEMOLECULES | colvar bias vatom setup generic |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | LOWER_WALLS DISTANCE UPPER_WALLS PRINT | colvar bias generic |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | MOLINFO COM PRINT LOWER_WALLS GYRATION DISTANCE PBMETAD ENERGY UPPER_WALLS | colvar bias vatom generic |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | ENSEMBLE MOLINFO ANTIBETARMSD CONTACTMAP PRINT METAD ALPHABETA SAXS STATS BIASVALUE CENTER GYRATION TORSION PBMETAD WHOLEMOLECULES | colvar bias multicolvar vatom isdb secondarystructure function generic |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | PRINT METAD COMMITTOR DUMPGRID MOVINGRESTRAINT LOAD REWEIGHT_METAD UPPER_WALLS HISTOGRAM UNITS CONVERT_TO_FES FLUSH COORDINATIONNUMBER | bias symfunc setup gridtools generic |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | ENERGY PRINT ENDPLUMED ECV_UMBRELLAS_LINE OPES_METAD TORSION ECV_MULTITHERMAL OPES_EXPANDED | colvar opes generic |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | READ DISTANCES MOLINFO PRINT RMSD DUMPGRID BIASVALUE HISTOGRAM EMMI CONVERT_TO_FES GROUP WHOLEMOLECULES | colvar core bias multicolvar isdb gridtools generic |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | PRINT COORDINATION CENTER PBMETAD WHOLEMOLECULES | colvar bias vatom generic |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | PRINT METAD DUMPGRID REWEIGHT_METAD MULTI_RMSD RESTRAINT HISTOGRAM CONVERT_TO_FES | colvar bias gridtools generic |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | PRINT ENERGY FISST BIASVALUE MATHEVAL GYRATION RESTRAINT DISTANCE UNITS GROUP | colvar core fisst bias setup function 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 CUSTOM ENDPLUMED COMBINE CENTER RESTRAINT DISTANCE TORSION GROUP | colvar core bias vatom function generic |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | RANDOM_EXCHANGES PRINT METAD INCLUDE TORSION | colvar bias generic |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | DISTANCES COM PRINT MOVINGRESTRAINT INPLANEDISTANCES FLUSH RESTART | bias multicolvar vatom setup generic |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | PRINT METAD COMBINE UPPER_WALLS LOWER_WALLS ENERGY DISTANCE FLUSH UNITS | colvar bias setup function generic |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | PRINT FCCUBIC METAD ENDPLUMED UPPER_WALLS UNITS CELL | colvar bias symfunc setup generic |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | DISTANCES PRINT METAD COMBINE UPPER_WALLS DISTANCE UNITS FLUSH RESTART | colvar bias multicolvar setup function generic |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | PRINT METAD MATHEVAL DISTANCE UPPER_WALLS UNITS FLUSH RESTART | colvar bias setup function generic |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | MOLINFO PRINT METAD ALPHABETA GYRATION UPPER_WALLS LOWER_WALLS GROUP WHOLEMOLECULES | colvar core bias multicolvar generic |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | MOLINFO PRINT METAD ALPHABETA COMMITTOR COMBINE FLUSH | bias function multicolvar generic |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | ENSEMBLE DIHCOR MOLINFO PRINT METAINFERENCE ALPHABETA ENDPLUMED STATS CENTER TORSION DISTANCE PBMETAD UPPER_WALLS DHENERGY GROUP RDC RESTRAINT WHOLEMOLECULES | colvar core bias multicolvar vatom isdb function generic |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | MOLINFO PRINT RMSD METAD ENDPLUMED ERMSD WHOLEMOLECULES | colvar bias generic |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | MOLINFO PRINT METAINFERENCE CS2BACKBONE RDC GROUP WHOLEMOLECULES | core isdb generic |
| 26.014 | Dissociation free energy (DFE) calculationsfor GPR15L–polySia | bio | metadynamics, protein-carbohydrate interaction | Davide Luciano and Gaston Courtade | GROUP PRINT METAD DISTANCE COM UPPER_WALLS | generic vatom colvar core bias |
| 26.008 | Ensemble Dynamics | methods | State Exploration, Protein Folding, Drug Binding, Phase Transition | Florian M. Dietrich | GROUP CUSTOM CELL UNITS PRINT BIASVALUE OPES_METAD_EXPLORE DISTANCE TORSION LOAD POSITION | generic setup opes colvar function core bias |
| 26.007 | Metadynamics Simulations Reveal the Protonation-Dependent Conformational Landscape of GSK-3β Dual Inhibitors | chemistry | metadynamics, ligand unbinding, path CVs, funnel metadynamics | Gian Marco Elisi | FUNNEL_PS ENDPLUMED FUNNEL MOLINFO UNITS MATHEVAL WHOLEMOLECULES METAD PRINT PATHMSD DISTANCE ANGLE RMSD COMBINE COM UPPER_WALLS LOWER_WALLS | generic vatom setup function colvar funnel bias |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | ENERGY GROUP ENDPLUMED CUSTOM UPPER_WALLS MOLINFO UNITS PYTORCH_MODEL METAD PRINT WHOLEMOLECULES POSITION DISTANCE BIASVALUE RMSD TORSION OPES_METAD LOWER_WALLS | generic setup pytorch opes colvar function core bias |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | CUSTOM PYTORCH_MODEL METAD COMBINE RMSD GROUP CONTACTMAP ENDPLUMED INCLUDE BIASVALUE COORDINATION FIT_TO_TEMPLATE MOLINFO PRINT POSITION DISTANCE OPES_METAD_EXPLORE OPES_METAD UPPER_WALLS CENTER ENERGY MATHEVAL UNITS WHOLEMOLECULES FLUSH FIXEDATOM LOWER_WALLS | generic vatom setup pytorch opes colvar function core bias |
| 24.018 | A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations | chemistry | prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning | Léon HUET | DISTANCE PRINT | generic colvar |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | ANN FIT_TO_TEMPLATE ALPHARMSD MOLINFO WHOLEMOLECULES PRINT METAD COMBINE POSITION | generic function colvar annfunc secondarystructure bias |
| 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 WRAPAROUND FIT_TO_TEMPLATE DISTANCES MOLINFO WHOLEMOLECULES PRINT METAD SHADOW UPPER_WALLS POSITION CENTER | generic vatom colvar multicolvar core isdb bias |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | PBMETAD UPPER_WALLS PRINT DISTANCE COM GYRATION | generic vatom colvar bias |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | PBMETAD INCLUDE RESTRAINT WHOLEMOLECULES PRINT TORSION COM GYRATION COORDINATION | generic vatom colvar bias |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | MOLINFO HISTOGRAM PRINT METAD READ TORSION CONVERT_TO_FES PUCKERING DUMPGRID | generic gridtools colvar bias |
| 22.027 | Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain | Max Bonomi | RMSD PRINT | generic colvar |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | PBMETAD UPPER_WALLS MOLINFO PRINT DISTANCE COM GYRATION | generic vatom colvar bias |
| 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 | ENERGY GROUP GYRATION PARABETARMSD ALPHARMSD MOLINFO WHOLEMOLECULES PRINT METAD DIHCOR ANTIBETARMSD UPPER_WALLS RANDOM_EXCHANGES LOWER_WALLS COORDINATION | generic colvar multicolvar secondarystructure core bias |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | ENERGY CONSTANT CUSTOM INCLUDE UNITS METAD PRINT DISTANCE BIASVALUE TORSION REWEIGHT_METAD | generic setup colvar function bias |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | READ METAD RMSD GROUP ENDPLUMED HISTOGRAM COM REWEIGHT_METAD COORDINATION PRINT DISTANCE CONVERT_TO_FES UPPER_WALLS MATHEVAL WHOLEMOLECULES FIXEDATOM FLUSH POSITION DUMPGRID | generic vatom colvar function core gridtools bias |
| 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 | |
| 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 | ENVIRONMENTSIMILARITY MATHEVAL PRINT Q6 VOLUME TD_WELLTEMPERED VES_LINEAR_EXPANSION UPPER_WALLS RESTART BF_LEGENDRE OPT_AVERAGED_SGD OPT_DUMMY | generic setup ves colvar symfunc function envsim bias |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | ENERGY GYRATION MOLINFO PRINT METAD DISTANCE COM UPPER_WALLS | generic vatom colvar bias |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | GROUP ENDPLUMED INCLUDE PRINT DISTANCE CENTER | generic core vatom colvar |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | SAXS PRINT FLUSH UPPER_WALLS CENTER MOLINFO DISTANCE WHOLEMOLECULES STATS PBMETAD METAINFERENCE TORSION GYRATION ENSEMBLE | vatom function isdb bias colvar generic |
| 25.005 | Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations | chemistry | WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD | Vikas Tiwari, Tarak Karmakar | COORDINATIONNUMBER COORDINATION RESTRAINT PRINT FLUSH ANGLE UPPER_WALLS LOWER_WALLS COMBINE DISTANCE METAD COM GROUP FIXEDATOM DISTANCES UNITS | vatom setup core function multicolvar symfunc bias colvar generic |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | PRINT ENERGY MOLINFO COMBINE DISTANCE WHOLEMOLECULES OPES_METAD GROUP ENDPLUMED MATHEVAL TORSION CUSTOM PYTORCH_MODEL COMMITTOR | core function opes colvar pytorch generic |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | FUNCPATHGENERAL PRINT UPPER_WALLS MOLINFO WHOLEMOLECULES DISTANCE COM GROUP METAD RESTART | vatom setup core function bias colvar generic |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | PRINT LOWER_WALLS CENTER UPPER_WALLS MOLINFO COMBINE SORT GHOST DISTANCE METAD WHOLEMOLECULES GROUP PUCKERING DISTANCES MATHEVAL POSITION GYRATION | vatom core function multicolvar bias 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 | DIHCOR COORDINATION PRINT FLUSH PARABETARMSD MOLINFO COMBINE WHOLEMOLECULES ALPHARMSD DISTANCE GROUP PBMETAD INCLUDE ENDPLUMED ANTIBETARMSD TORSION GYRATION | secondarystructure core function multicolvar bias 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 | COORDINATION PRINT LOWER_WALLS UPPER_WALLS CENTER MOLINFO COMBINE DEBUG DISTANCE METAD COM GROUP GHBFIX BIASVALUE | vatom core function bias colvar generic |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | COORDINATION PRINT READ HISTOGRAM DUMPGRID CONVERT_TO_FES METAD GROUP ENDPLUMED COMMITTOR | core bias colvar gridtools generic |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | COORDINATION PRINT UPPER_WALLS DISTANCE COM PBMETAD GYRATION | colvar bias generic vatom |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | PRINT FLUSH UPPER_WALLS COMBINE DISTANCE WHOLEMOLECULES COM METAD TORSION | vatom function bias colvar generic |
| 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 | ENVIRONMENTSIMILARITY PRINT ECV_UMBRELLAS_LINE DUMPGRID UPPER_WALLS LOWER_WALLS HISTOGRAM OPES_EXPANDED RESTART | setup envsim opes bias gridtools generic |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | ENVIRONMENTSIMILARITY PRINT ECV_UMBRELLAS_LINE UPPER_WALLS LOWER_WALLS INCLUDE OPES_EXPANDED RESTART | setup envsim opes bias generic |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | PRINT ENERGY DISTANCE WHOLEMOLECULES RMSD TORSION CONSTANT PYTORCH_MODEL COMMITTOR MOLINFO CONTACTMAP GROUP ENDPLUMED UNITS COMBINE OPES_METAD INCLUDE CUSTOM POSITION BIASVALUE | setup core function opes bias colvar pytorch generic |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | PRINT TORSION WHOLEMOLECULES | colvar generic |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | PRINT UPPER_WALLS LOWER_WALLS FUNNEL_PS DISTANCE WHOLEMOLECULES COM METAD PATHMSD FUNNEL | vatom funnel bias colvar generic |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | COORDINATION WHOLEMOLECULES GROUP PBMETAD UNITS | setup core bias colvar generic |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | PRINT FLUSH LOWER_WALLS UPPER_WALLS OPES_METAD GROUP LOAD MATHEVAL PYTORCH_MODEL | setup core function opes bias pytorch generic |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | COORDINATION PRINT ENERGY UPPER_WALLS CENTER ANGLE FIT_TO_TEMPLATE WHOLEMOLECULES DISTANCE OPES_METAD GROUP FIXEDATOM ENDPLUMED MATHEVAL PYTORCH_MODEL | vatom core function opes bias colvar pytorch generic |
| 20.021 | Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. | bio | phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution | Cristina Paissoni | COORDINATION RESTRAINT PRINT MOLINFO WHOLEMOLECULES STATS | function colvar bias generic |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | PRINT ENERGY UPPER_WALLS CENTER LOWER_WALLS MOLINFO COMBINE WHOLEMOLECULES METAD DISTANCE RMSD MATHEVAL | vatom function bias colvar generic |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | COORDINATIONNUMBER PRINT FLUSH COMBINE EXTERNAL METAD GROUP ENDPLUMED UNITS RESTART | setup core function symfunc bias generic |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | PRINT EXTERNAL METAD OPES_METAD ENDPLUMED UNITS TORSION POSITION | setup opes bias colvar generic |
| 19.046 | Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding | bio | VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation | Faidon Brotzakis | PRINT LOWER_WALLS UPPER_WALLS MOLINFO COMBINE ALPHABETA WHOLEMOLECULES DISTANCE COM GROUP METAD DISTANCES REWEIGHT_METAD RMSD FUNNEL TORSION BRIDGE | vatom funnel core function multicolvar bias colvar generic adjmat |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | PRINT FLUSH UPPER_WALLS CS2BACKBONE LOWER_WALLS MOLINFO ALPHABETA RESTART WHOLEMOLECULES GROUP PBMETAD ENDPLUMED ANTIBETARMSD BIASVALUE | setup core secondarystructure multicolvar isdb bias generic |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | PRINT EMMI MOLINFO GROUP BIASVALUE | isdb bias core generic |
| 26.013 | Characterizing Partially Unfolded States of the C-Terminal Domain in WT and 3PA Mouse Prion Protein | bio | parallel-bias metadynamics, PBMetaD, metadynamics, mouse prion protein, prion protein, protein folding, partially unfolded states, molecular dynamics | Sonali M. Jadhav | INCLUDE COM PBMETAD GYRATION CONTACTMAP DISTANCE GROUP WHOLEMOLECULES COORDINATION ALPHARMSD PRINT DUMPMASSCHARGE MOLINFO | vatom secondarystructure generic bias core colvar |
| 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 COM DUMPGRID CONVERT_TO_FES UPPER_WALLS DISTANCE REWEIGHT_BIAS LOWER_WALLS WHOLEMOLECULES HISTOGRAM PRINT FIXEDATOM MOLINFO | vatom gridtools bias generic colvar |
| 25.026 | Deciphering the Molecular Mechanisms of Startle Disease - the Role of the Asn46Lys Mutation in the Glycine Receptor | bio | metadynamics, glycine receptors, funnel metadynamics | Jacob Adam Clark | FUNNEL_PS METAD COM UPPER_WALLS FUNNEL LOWER_WALLS PRINT | funnel bias vatom generic |
| 25.025 | Enhanced Sampling of Ligand Binding Coupled to RNA Conformational Dynamics | bio | OPES, OPES Flooding , Metadynamics, RNA, Ligand binding, Free Energy, Kinetics, Funnel | Revanth Elangovan and Dhiman Ray | ENDPLUMED METAD OPES_METAD WRAPAROUND TORSION CENTER CUSTOM GROUP WHOLEMOLECULES COMMITTOR COM FUNNEL COORDINATION FUNNEL_PS MATHEVAL DISTANCE PRINT UPPER_WALLS LOWER_WALLS RMSD | vatom function funnel bias opes core generic colvar |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | METAD PUCKERING TORSION RESTART PRINT MOLINFO | bias setup generic colvar |
| 24.021 | Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state | chemistry | ion pairing, caco3, opes, proton transfer, crystallization | Pablo Piaggi | OPES_METAD ENERGY UPPER_WALLS DISTANCE COORDINATION PRINT | bias opes generic colvar |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | INCLUDE ENERGY CONTACTMAP UPPER_WALLS WHOLEMOLECULES OPES_EXPANDED PRINT ECV_MULTITHERMAL MOLINFO | bias opes generic colvar |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | INCLUDE ALPHABETA COM TORSION GYRATION DISTANCE WHOLEMOLECULES COORDINATION MOVINGRESTRAINT PRINT | vatom multicolvar bias generic colvar |
| 23.045 | Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state | bio | Path CVs Metadynamics, GPCRs activation transition | Vittorio Limongelli | INCLUDE METAD PATHMSD CONTACTMAP FUNCPATHMSD UPPER_WALLS DISTANCE LOWER_WALLS ALPHARMSD PRINT MOLINFO | function secondarystructure bias generic 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 | INCLUDE WRAPAROUND UPPER_WALLS DISTANCE GROUP WHOLEMOLECULES PRINT BIASVALUE EMMIVOX MOLINFO | isdb generic bias core colvar |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | DFSCLUSTERING COORDINATIONNUMBER UNITS CONTACT_MATRIX DENSITY AROUND CLUSTER_NATOMS GROUP LOAD Q3 PRINT LOCAL_AVERAGE FIXEDATOM DUMPGRID HISTOGRAM RESTRAINT LOCAL_Q3 CLUSTER_DISTRIBUTION | adjmat vatom setup volumes gridtools generic bias symfunc core clusters |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | LOCAL_AVERAGE METAD VOLUME ENERGY UNITS UPPER_WALLS PIV PAIRENTROPY CUSTOM FUNCPATHMSD Q6 PRINT RESTRAINT Q4 | function setup piv gridtools bias symfunc generic colvar |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | COM PBMETAD GYRATION UPPER_WALLS DISTANCE PRINT MOLINFO | bias vatom generic colvar |
| 22.021 | Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn Løland Bore | INCLUDE ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE UPPER_WALLS LOWER_WALLS OPES_EXPANDED PRINT | envsim opes bias generic |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | ENDPLUMED METAD COORDINATIONNUMBER TORSION CENTER DISTANCE COMMITTOR PRINT | vatom bias symfunc generic colvar |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | METAD UNITS TORSION UPPER_WALLS CUSTOM LOAD LOWER_WALLS CONSTANT MOVINGRESTRAINT PRINT COMBINE RESTRAINT ENSEMBLE | function setup bias generic colvar |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | INCLUDE METAD COORDINATIONNUMBER VOLUME ENERGY CENTER LOAD GROUP PRINT COMBINE | vatom function setup bias symfunc core generic colvar |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | INCLUDE METAD UPPER_WALLS CONSTANT MOVINGRESTRAINT PRINT COMBINE RESTRAINT | function bias generic |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | DFSCLUSTERING COORDINATIONNUMBER DUMPGRID CONTACT_MATRIX DENSITY MFILTER_MORE AROUND CLUSTER_NATOMS GROUP LOAD MULTICOLVARDENS PRINT FIXEDATOM RESTRAINT CLUSTER_DISTRIBUTION | adjmat vatom multicolvar setup volumes gridtools generic bias symfunc core clusters |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | PBMETAD MATHEVAL TORSION WHOLEMOLECULES CONSTANT RESTART PRINT BIASVALUE | function setup bias generic colvar |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | ENDPLUMED TORSION POSITION CUSTOM WHOLEMOLECULES ECV_MULTITHERMAL_MULTIBARIC ECV_MULTITHERMAL MOLINFO OPES_EXPANDED VOLUME ENERGY MATHEVAL LOAD PRINT ECV_LINEAR UNITS ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY UPPER_WALLS Q6 RMSD | envsim function setup bias symfunc opes generic colvar |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | TD_WELLTEMPERED VES_LINEAR_EXPANSION FLUSH DUMPGRID ANGLE UNITS OPT_AVERAGED_SGD UPPER_WALLS CONVERT_TO_FES TD_GRID DISTANCE LOWER_WALLS COORDINATION HISTOGRAM BF_CHEBYSHEV PRINT COMBINE EXTERNAL | ves function setup gridtools bias generic colvar |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | METAD COM ENERGY GYRATION UPPER_WALLS DISTANCE PRINT MOLINFO | bias vatom generic colvar |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | METAD PATHMSD UPPER_WALLS WHOLEMOLECULES LOWER_WALLS PRINT | bias generic colvar |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | METAD ENERGY GYRATION WHOLEMOLECULES PRINT | bias generic colvar |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | METAD COM UPPER_WALLS CENTER DISTANCE GROUP LOWER_WALLS RESTART PRINT | vatom setup generic bias core colvar |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | DISTANCES METAD FLUSH UPPER_WALLS PATH RESTART PRINT | multicolvar setup mapping bias generic |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | METAD ENERGY GROUP COORDINATION EXTERNAL | bias core colvar |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | METAD TORSION GYRATION WHOLEMOLECULES PRINT | bias generic colvar |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | METAD MATHEVAL TORSION WHOLEMOLECULES CONSTANT PRINT BIASVALUE | function bias generic colvar |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | ENDPLUMED INCLUDE STATS UPPER_WALLS CENTER DISTANCE GROUP WHOLEMOLECULES RMSD PRINT SAXS RESTRAINT BIASVALUE MOLINFO | isdb vatom function bias core generic colvar |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | ENDPLUMED METAD VES_DELTA_F ENERGY UNITS TORSION POSITION LOAD RESTART PRINT | ves setup bias generic colvar |
| 26.016 | Cryo-EM ensemble of the PilQ secretin | bio | EMMIVox, cryo-EM, ensemble | Tatiana I. Morozova | GROUP WHOLEMOLECULES MOLINFO PRINT BIASVALUE EMMIVOX | bias isdb generic core |
| 26.010 | Solvation-Mediated Ammonia Synthesis in a Nanoheterogeneous Liquid Alloy | materials | OPES, Catalysis, Ammonia Synthesis | Axel Tosello Gardini | FLUSH CUSTOM COORDINATIONNUMBER GROUP DISTANCE OPES_METAD OPES_METAD_EXPLORE UNITS DISTANCES COORDINATION UPPER_WALLS PRINT INCLUDE | symfunc setup bias colvar generic core opes multicolvar function |
| 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 | FUNNEL_PS GROUP DISTANCE ENERGY LOWER_WALLS PYTORCH_MODEL FUNNEL COM COORDINATION WHOLEMOLECULES RMSD UPPER_WALLS PRINT METAD MATHEVAL WRAPAROUND | vatom pytorch funnel bias colvar generic core function |
| 26.000 | OPES simulations of disordered proteins | bio | OPES, IDPs | Julian Streit | ENERGY ECV_MULTITHERMAL RESTART OPES_EXPANDED PRINT | opes setup colvar generic |
| 25.023 | Molecular simulations of Tau-protein oligomers | bio | metadynamics, proteins, aggregation | Giovanni Bussi | FLUSH DUMPGRID CONVERT_TO_FES REWEIGHT_BIAS RESTART RMSD CONTACTMAP HISTOGRAM PRINT CUSTOM RESTRAINT METAD | gridtools setup bias colvar generic function |
| 25.014 | Atomic resolution ensembles of intrinsically disordered proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | GROUP BAIES PRINT BIASVALUE | bias isdb generic core |
| 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 | DUMPATOMS DISTANCE TORSION PBMETAD ENERGY READ VOLUME CENTER RESTART UPDATE_IF WHOLEMOLECULES MOLINFO PRINT INCLUDE GYRATION | vatom setup bias colvar generic |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | ENDPLUMED ABMD UNITS UPPER_WALLS PRINT PATHMSD | setup bias colvar 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 | COMMITTOR GROUP DISTANCE OPES_METAD LOWER_WALLS RESTART COORDINATION UNITS UPPER_WALLS PRINT CUSTOM | setup bias colvar generic core opes function |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | RESTRAINT POSITION UNITS PRINT | setup bias colvar generic |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | COMBINE ERMSD ENERGY OPES_METAD_EXPLORE VOLUME PYTORCH_MODEL RESTART COORDINATION ECV_MULTITHERMAL MOLINFO OPES_EXPANDED PRINT | pytorch setup colvar generic opes function |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | FLUSH TORSION RESTART WHOLEMOLECULES PRINT METAD | setup bias colvar generic |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | READ RMSD MATHEVAL FLUSH DISTANCE CONVERT_TO_FES REWEIGHT_METAD ENDPLUMED COM MOLINFO HISTOGRAM WRAPAROUND GROUP DUMPGRID WHOLEMOLECULES PRINT METAD FIT_TO_TEMPLATE COMMITTOR FIXEDATOM COORDINATION PATH UPPER_WALLS CONTACTMAP INCLUDE | core vatom gridtools mapping bias colvar generic function |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | DFSCLUSTERING CONTACT_MATRIX CLUSTER_NATOMS CLUSTER_PROPERTIES UNITS UPPER_WALLS PRINT COORDINATIONNUMBER METAD | adjmat symfunc setup bias generic clusters |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | COMBINE DISTANCE UNITS WHOLEMOLECULES PRINT METAD | setup bias colvar generic function |
| 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 | CONSTANT DISTANCE LOWER_WALLS CENTER WHOLEMOLECULES UPPER_WALLS PRINT BIASVALUE MATHEVAL METAD | vatom bias colvar generic function |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | INCLUDE GROUP CENTER LOAD PRINT COORDINATIONNUMBER METAD | symfunc vatom setup bias generic core |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | FLUSH CUSTOM COMMITTOR GROUP FIXEDATOM DISTANCE ENERGY OPES_METAD LOWER_WALLS ZDISTANCES UNITS COM DISTANCES UPPER_WALLS PRINT COORDINATIONNUMBER MATHEVAL | symfunc vatom setup bias colvar generic core opes multicolvar function |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | ANGLE DISTANCE LOWER_WALLS COM WHOLEMOLECULES UPPER_WALLS MOVINGRESTRAINT PRINT METAD | vatom bias colvar generic |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | POSITION TORSION ENERGY OPES_METAD ECV_MULTITHERMAL ENDPLUMED UNITS OPES_EXPANDED PRINT | opes setup colvar generic |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | LOWER_WALLS WHOLEMOLECULES UPPER_WALLS PCAVARS PRINT METAD | mapping bias generic |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | FLUSH COMBINE CUSTOM GROUP GHBFIX COORDINATION MOLINFO UPPER_WALLS LOAD PRINT BIASVALUE METAD | setup bias colvar generic core function |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | FLUSH COMMITTOR COORDINATIONNUMBER DUMPGRID CONVERT_TO_FES LOAD VOLUME REWEIGHT_BIAS UNITS BIASVALUE UPPER_WALLS RESTRAINT HISTOGRAM MOVINGRESTRAINT PRINT CUSTOM ANN | symfunc gridtools annfunc setup bias colvar generic function |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | GROUP WHOLEMOLECULES MOLINFO LOAD PRINT BIASVALUE EMMIVOX | core isdb setup bias generic |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | FLUSH FIT_TO_TEMPLATE COMBINE ANGLE GROUP DISTANCE BRIDGE LOWER_WALLS RMSD UNITS COORDINATION WHOLEMOLECULES DISTANCES UPPER_WALLS PRINT METAD MATHEVAL | adjmat setup bias colvar generic core multicolvar function |
| 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 | FLUSH COMBINE COORDINATIONNUMBER DISTANCE LOWER_WALLS UNITS COORDINATION COM UPPER_WALLS METAD GYRATION | symfunc vatom setup bias colvar generic function |
| 22.005 | Collective Variable for Metadynamics Derived from AlphaFold Output | bio | AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable | Vojtech Spiwok | LOAD PRINT METAD WHOLEMOLECULES | setup bias generic |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | COMBINE PRINT COORDINATION WHOLEMOLECULES MOLINFO ERMSD BIASVALUE METAD | bias colvar function generic |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | FUNNEL_PS DISTANCE LOWER_WALLS FUNNEL COM UPPER_WALLS PRINT METAD | vatom funnel bias colvar generic |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | INCLUDE RANDOM_EXCHANGES GROUP DISTANCE DUMPGRID ENERGY REWEIGHT_METAD LOWER_WALLS COORDINATION WHOLEMOLECULES MOLINFO UPPER_WALLS HISTOGRAM PRINT METAD PUCKERING | gridtools bias colvar generic core |
| 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 DISTANCE COM WHOLEMOLECULES PRINT | vatom colvar generic core |
| 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 | COMBINE STATS COORDINATION WHOLEMOLECULES MOLINFO RESTRAINT PRINT | bias colvar function generic |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | PAIRENTROPY ENERGY VOLUME UNITS LOAD FLUSH DISTANCE CONTACT_MATRIX CONVERT_TO_FES REWEIGHT_METAD CENTER HISTOGRAM COMBINE SPRINT DUMPGRID Q6 REWEIGHT_BIAS LOCAL_AVERAGE PRINT METAD LOWER_WALLS DENSITY COORDINATION UPPER_WALLS COORDINATIONNUMBER | adjmat symfunc vatom gridtools volumes setup bias colvar generic function sprint |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | GROUP DISTANCE CENTER COORDINATION RESTART WHOLEMOLECULES DISTANCES PRINT | core vatom setup colvar generic multicolvar |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | COMBINE DISTANCE TORSION RMSD RESTART WHOLEMOLECULES MOLINFO UPPER_WALLS PRINT METAD | setup bias colvar generic function |
| 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 | COMBINE DISTANCE DUMPGRID CONVERT_TO_FES REWEIGHT_METAD LOWER_WALLS READ ENDPLUMED ABMD COM UPPER_WALLS HISTOGRAM PRINT METAD MATHEVAL | vatom gridtools bias colvar generic function |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | ERMSD DISTANCE TORSION RMSD WHOLEMOLECULES MOLINFO PRINT METAD | bias colvar generic |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | COMBINE ANGLE INCLUDE ENSEMBLE GROUP STATS ENDPLUMED CENTER COORDINATION SAXS WHOLEMOLECULES MOLINFO BIASVALUE MATHEVAL PRINT ALPHABETA PBMETAD | isdb vatom bias colvar generic core multicolvar function |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | CONSTANT DISTANCE LOWER_WALLS COM WHOLEMOLECULES UPPER_WALLS PRINT BIASVALUE MATHEVAL METAD | vatom bias colvar generic function |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | DISTANCE ENDPLUMED RMSD COM WHOLEMOLECULES FUNCPATHMSD CONTACTMAP PRINT METAD | vatom bias colvar generic function |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | GROUP DISTANCE TORSION COM RESTRAINT PRINT | core vatom bias colvar generic |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | DISTANCE LOWER_WALLS COM WHOLEMOLECULES UPPER_WALLS PRINT METAD | vatom bias colvar generic |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | TORSION DRR PRINT | colvar generic drr |
| 26.015 | Ensemble Dynamics | methods | State Exploration, Protein Folding, Drug Binding, Phase Transition | Florian M. Dietrich | BIASVALUE PRINT POSITION UNITS CELL OPES_METAD_EXPLORE CUSTOM TORSION GROUP DISTANCE LOAD | generic opes colvar function core bias setup |
| 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 | PRINT ENERGY COORDINATION UPPER_WALLS CENTER OPES_METAD_EXPLORE GROUP DISTANCE FIXEDATOM WHOLEMOLECULES MATHEVAL ANGLE FIT_TO_TEMPLATE | generic opes colvar function vatom core bias |
| 25.007 | Shaping the glycan landscape. Hidden relationships between linkage and ring distortion induced by carbohydrate-active enzmyes | bio | REST-RECT, REST2, glycan, enzyme, CAZyme, steered | Isabell Grothaus | PRINT RESTRAINT PUCKERING TORSION DISTANCE RESTART METAD MOLINFO MOVINGRESTRAINT | generic colvar bias setup |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | COMBINE WHOLEMOLECULES ERMSD METAD MOLINFO | generic colvar bias function |
| 24.020 | Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics | bio | LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning | Ziyue Zou, Dedi Wang, Pratyush Tiwary | PRINT COMMITTOR TORSION GROUP METAD LOAD | generic colvar core bias setup |
| 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 | PRINT DRR COORDINATION FLUSH LOWER_WALLS UPPER_WALLS METAD WHOLEMOLECULES RMSD PYTORCH_MODEL MOLINFO | generic colvar drr pytorch bias |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | BIASVALUE PRINT UNITS CUSTOM DISTANCE | generic colvar function bias setup |
| 23.043 | Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling | materials | Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters | Lorenzo Gigli | PRINT FLUSH SUM TRANSPOSE SELECT_COMPONENTS MATHEVAL METAD INCLUDE | generic valtools function matrixtools bias |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | PRINT ENERGY Q4 COORDINATIONNUMBER COMBINE MATHEVAL Q6 METAD VOLUME | generic symfunc colvar function bias |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | PRINT COORDINATIONNUMBER LOWER_WALLS COMBINE LOCAL_Q6 GROUP Q6 METAD MFILTER_MORE MOVINGRESTRAINT | generic symfunc function core multicolvar bias |
| 23.013 | Path meta-eABF simulation of large scale conformational change in STING protein | methods | meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint | Istvan Kolossvary | PATHMSD BIASVALUE DRR PRINT UNITS UPPER_WALLS LOWER_WALLS FLUSH CUSTOM METAD TIME | generic colvar function drr bias setup |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | PRINT PBMETAD TORSION GROUP WHOLEMOLECULES GYRATION MOLINFO | generic colvar bias core |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | PRINT ALPHARMSD COM METAD DISTANCE CONTACTMAP DUMPFORCES MOLINFO ANGLE | generic colvar vatom bias secondarystructure |
| 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 | PRINT ENERGY UPPER_WALLS LOWER_WALLS WHOLEMOLECULES CONTACTMAP METAD | generic colvar bias |
| 22.034 | Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods | materials | metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene | Matteo Salvalaglio | PRINT COMMITTOR CELL LOWER_WALLS UPPER_WALLS DRMSD CUSTOM MATHEVAL METAD | generic colvar bias function |
| 22.032 | Reciprocal barrier restraint. Application to path-meta-eABF | methods | restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC | Istvan Kolossvary | PATHMSD BIASVALUE DRR PRINT FLUSH CUSTOM METAD | generic colvar function drr bias |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | PRINT ALPHARMSD PBMETAD COM ALPHABETA TORSION RESTART WHOLEMOLECULES MOLINFO ANTIBETARMSD | generic colvar setup vatom multicolvar bias secondarystructure |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | PRINT RMSD | generic colvar |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | PRINT COMMITTOR COORDINATIONNUMBER COM COMBINE DISTANCE WHOLEMOLECULES RMSD METAD MOLINFO | generic symfunc colvar function vatom bias |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | PRINT ECV_MULTITHERMAL ENERGY BIASVALUE POSITION PBMETAD UNITS LOWER_WALLS OPES_METAD_EXPLORE UPPER_WALLS CUSTOM ENDPLUMED TORSION OPES_METAD METAD OPES_EXPANDED ECV_UMBRELLAS_FILE | generic opes colvar function bias setup |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | PRINT ENERGY ALPHARMSD UPPER_WALLS LOWER_WALLS DISTANCE WHOLEMOLECULES MATHEVAL CONTACTMAP METAD MOLINFO INCLUDE | generic colvar function bias secondarystructure |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | PRINT ALPHARMSD PBMETAD REWEIGHT_BIAS ALPHABETA GROUP RESTART WHOLEMOLECULES CONTACTMAP METAD MOLINFO | generic colvar setup core multicolvar bias secondarystructure |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | COORDINATION UPPER_WALLS COORDINATIONNUMBER EXTERNAL REWEIGHT_METAD REWEIGHT_BIAS BF_CHEBYSHEV TD_GRID COMBINE DISTANCES CONVERT_TO_FES LOAD RESTRAINT FLUSH UNITS VES_LINEAR_EXPANSION UWALLS DISTANCE HISTOGRAM OPT_AVERAGED_SGD PRINT ANGLES LOWER_WALLS METAD DUMPGRID | generic symfunc colvar function setup ves multicolvar bias gridtools |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | BIASVALUE PRINT ALPHARMSD FLUSH PBMETAD EEFSOLV CENTER SAXS GROUP WHOLEMOLECULES GYRATION MOLINFO METAINFERENCE | generic isdb colvar vatom core bias secondarystructure |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | PRINT CENTER DISTANCE RESTART METAD FIT_TO_TEMPLATE | generic colvar vatom bias setup |
| 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 | TORSION PRINT DISTANCE METAD | generic colvar bias |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | TORSION PRINT METAD | generic colvar 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 | BIASVALUE PRINT LOWER_WALLS COM PROJECTION_ON_AXIS UPPER_WALLS GROUP CONSTANT DISTANCE WHOLEMOLECULES MATHEVAL CONTACTMAP METAD MOLINFO FUNCPATHGENERAL LOAD INCLUDE | generic colvar function vatom core bias setup |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | PRINT FLUSH PBMETAD CENTER SAXS STATS ALPHABETA TORSION DISTANCE WHOLEMOLECULES GYRATION MOLINFO METAINFERENCE ENSEMBLE | generic isdb colvar function vatom multicolvar bias |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | PRINT UNITS COM UPPER_WALLS LOWER_WALLS FLUSH ENDPLUMED TORSION GROUP DISTANCE OPES_METAD MATHEVAL PYTORCH_MODEL LOAD | generic opes colvar function pytorch vatom core bias setup |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | PRINT UNITS ENDPLUMED GYRATION MOVINGRESTRAINT | generic colvar bias 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 | PRINT ENERGY UPPER_WALLS LOWER_WALLS COORDINATIONNUMBER ENDPLUMED DISTANCES GYRATION METAD | generic symfunc colvar multicolvar bias |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | PRINT POSITION UNITS MAZE_SIMULATED_ANNEALING MAZE_LOSS MAZE_OPTIMIZER_BIAS | maze generic colvar setup |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | FIND_CONTOUR_SURFACE UNITS CENTER FOURIER_TRANSFORM MORE_THAN GROUP FCCUBIC MULTICOLVARDENS DUMPGRID | gridtools symfunc function contour vatom core fourier setup |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | PRINT ENDPLUMED TORSION MATHEVAL METAD | generic colvar bias function |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | CLUSTER_WITHSURFACE COMMITTOR OUTPUT_CLUSTER FLUSH LOCAL_Q6 CONTACT_MATRIX ENDPLUMED CLUSTER_NATOMS DFSCLUSTERING Q6 MFILTER_MORE | adjmat generic symfunc clusters multicolvar |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | PRINT EDS RESTRAINT COMBINE TORSION DISTANCE | generic colvar eds function bias |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | BIASVALUE PUCKERING TORSION CONSTANT MATHEVAL MOLINFO INCLUDE | generic colvar bias function |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | PRINT COORDINATION PBMETAD CENTER CS2BACKBONE ALPHABETA GROUP DISTANCE WHOLEMOLECULES GYRATION MOLINFO METAINFERENCE INCLUDE | generic isdb colvar vatom core multicolvar bias |
| 26.012 | Buprenorphine Restricts the Conformational Landscape of the μ-Opioid Receptor | bio | OneOPES, GPCR, MOR, activation, euclidean path, conformational changes, allostery | Simone Aureli | RMSD COORDINATION UPPER_WALLS OPES_EXPANDED OPES_METAD_EXPLORE GROUP ENERGY VOLUME CENTER PRINT ECV_MULTITHERMAL CUSTOM PATH DISTANCE | vatom colvar bias function generic mapping opes core |
| 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 | RMSD COORDINATION LOWER_WALLS UPPER_WALLS OPES_EXPANDED OPES_METAD_EXPLORE GHOST GROUP ENERGY PRINT ECV_MULTITHERMAL DISTANCES CUSTOM DISTANCE PATHMSD CENTER | vatom colvar bias function multicolvar generic opes core |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | LOWER_WALLS UPPER_WALLS RESTART MULTI_RMSD PRINT MATHEVAL DISTANCE PBMETAD UNITS | colvar function bias setup generic |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | FLUSH COMMITTOR WHOLEMOLECULES COM GROUP PRINT ABMD DISTANCE | vatom colvar bias generic core |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | COORDINATION TORSION OPES_METAD LOAD GROUP ENERGY PRINT COMBINE CUSTOM DISTANCE | colvar function setup generic opes core |
| 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 | FIT_TO_TEMPLATE METAD UPPER_WALLS WHOLEMOLECULES GROUP COMBINE DISTANCE FIXEDATOM ENDPLUMED PRINT MATHEVAL ANGLE COORDINATION TORSION RMSD MOLINFO OPES_METAD CONTACTMAP COMMITTOR CUSTOM CENTER | vatom function bias colvar generic opes core |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | TORSION GROUP PRINT METAD UNITS | bias colvar setup generic core |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | TORSION RESTART PRINT METAD UNITS | bias colvar setup generic |
| 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 | FLUSH OPES_METAD UPPER_WALLS GROUP ZDISTANCES PRINT COORDINATIONNUMBER DISTANCE FIXEDATOM UNITS | symfunc vatom bias colvar multicolvar setup generic opes 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 | COORDINATION TORSION LOWER_WALLS UPPER_WALLS OPES_METAD OPES_METAD_EXPLORE WHOLEMOLECULES FIT_TO_TEMPLATE GROUP CENTER PRINT PYTORCH_MODEL CUSTOM PATH FIXEDATOM UNITS DISTANCE | vatom colvar bias function pytorch setup generic mapping opes core |
| 23.010 | An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands | bio | GPCR, binding free energy, free energy surface | Timothy Clark | LOWER_WALLS UPPER_WALLS WHOLEMOLECULES CONSTANT BIASVALUE PRINT MATHEVAL DISTANCE METAD | function bias generic colvar |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | MFILTER_LESS Q4 CONTACT_MATRIX LOCAL_AVERAGE LOCAL_Q4 Q6 GROUP DFSCLUSTERING CLUSTER_NATOMS PRINT MFILTER_MORE COORDINATIONNUMBER COMBINE LOCAL_Q6 | symfunc function multicolvar adjmat generic clusters core |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | Q4 LOAD Q6 GROUP PRINT MATHEVAL INCLUDE COORDINATIONNUMBER COMBINE PAIRENTROPY METAD CENTER | symfunc vatom function bias setup generic gridtools core |
| 22.035 | Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties | bio | intrinsically disordered proteins, parallel bias metadynamics, protein | Kresten Lindorff-Larsen | TORSION MOLINFO WHOLEMOLECULES GYRATION PBMETAD | colvar generic bias |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | FLUSH COM BIASVALUE PRINT DRR CUSTOM DISTANCE METAD UNITS | vatom function bias colvar setup drr generic |
| 22.023 | Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy | bio | CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble | Faidon Brotzakis | RMSD TORSION COORDINATION MOLINFO UPPER_WALLS RESTART WHOLEMOLECULES COM GROUP EMMI BIASVALUE PRINT PBMETAD | vatom colvar bias setup isdb generic core |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | COORDINATION FLUSH UPPER_WALLS LOAD COMMITTOR WHOLEMOLECULES FIT_TO_TEMPLATE GROUP ENERGY PRINT MATHEVAL PYTORCH_MODEL ANGLE DISTANCE FIXEDATOM ENDPLUMED CENTER | vatom colvar bias function pytorch setup generic core |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | COORDINATION CONTACTMAP MOLINFO RANDOM_EXCHANGES ALPHARMSD PRINT ANTIBETARMSD INCLUDE DISTANCE METAD UNITS CENTER | vatom colvar bias setup secondarystructure generic |
| 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 UPPER_WALLS WHOLEMOLECULES GYRATION GROUP PRINT ALPHABETA ENDPLUMED METAD | colvar bias multicolvar generic core |
| 21.043 | Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes | chemistry | well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability | Huixia Lu | TORSION FIT_TO_TEMPLATE PRINT FIXEDATOM METAD | vatom colvar generic bias |
| 21.041 | Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics | methods | metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions | Matej Badin | COORDINATION VOLUME PRINT COMBINE CUSTOM ENDPLUMED METAD | function colvar generic bias |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | RESTRAINT LOAD GROUP PRINT DISTANCE FIXEDATOM | vatom colvar bias setup generic core |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | LOWER_WALLS UPPER_WALLS WHOLEMOLECULES COM PRINT DISTANCE METAD UNITS | vatom colvar bias setup generic |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | LOWER_WALLS LOAD FIT_TO_TEMPLATE UPPER_WALLS WHOLEMOLECULES GROUP DISTANCES DISTANCE FIXEDATOM ENDPLUMED PRINT MATHEVAL ANGLE COORDINATION TORSION OPES_METAD PYTORCH_MODEL UNITS CENTER | vatom bias colvar function multicolvar pytorch setup generic opes core |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | TORSIONS COM PRINT MATHEVAL DISTANCE KDE | vatom colvar function multicolvar generic gridtools |
| 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 | COORDINATION RESTRAINT RESTART WHOLEMOLECULES CENTER PRINT MATHEVAL POSITION METAD REWEIGHT_BIAS | vatom colvar bias function setup 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 | LOWER_WALLS UPPER_WALLS RESTART WHOLEMOLECULES PRINT PATHMSD METAD | colvar bias setup generic |
| 21.002 | Phase equilibrium of water with hexagonal and cubic ice using the SCAN functional | materials | ice, water, SCAN, OPES, VES, multithermal, crystallization, environment similarity, refcv, reweighting | Pablo Piaggi | ECV_MULTITHERMAL_MULTIBARIC BF_LEGENDRE OPES_EXPANDED UPPER_WALLS Q6 RESTART ENERGY VOLUME ENVIRONMENTSIMILARITY PRINT VES_LINEAR_EXPANSION MATHEVAL ECV_UMBRELLAS_LINE TD_UNIFORM OPT_AVERAGED_SGD | symfunc bias colvar function envsim setup ves generic opes |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | TORSION ENDPLUMED PRINT | colvar generic |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | TORSION LOWER_WALLS UPPER_WALLS LOAD GROUP ENERGY PRINT COMBINE DISTANCES DISTANCE UNITS | colvar bias function multicolvar setup generic core |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | EMMIVOX MOLINFO DUMPATOMS LOAD WHOLEMOLECULES GROUP BIASVALUE PRINT | bias setup isdb generic core |
| 20.014 | amyloid beta small molecule interaction | bio | intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta | Gabriella Heller | FLUSH STATS ALPHARMSD PARABETARMSD METAINFERENCE WHOLEMOLECULES GYRATION GROUP INCLUDE COMBINE ENDPLUMED CS2BACKBONE PRINT DIHCOR PBMETAD COORDINATION TORSION MOLINFO ENSEMBLE ANTIBETARMSD | colvar function bias multicolvar isdb secondarystructure generic core |
| 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 | FLUSH LOWER_WALLS HISTOGRAM REWEIGHT_METAD METAD UPPER_WALLS WHOLEMOLECULES READ COMBINE DISTANCE ENDPLUMED DUMPGRID COM FUNCPATHMSD PRINT CONTACTMAP MOLINFO CONVERT_TO_FES ABMD | vatom function bias colvar generic gridtools |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_LOSS PRINT MAZE_SIMULATED_ANNEALING POSITION MAZE_OPTIMIZER_BIAS UNITS | setup colvar generic maze |
| 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 | COORDINATION FLUSH LOWER_WALLS UPPER_WALLS RESTART GROUP PRINT POSITION METAD UNITS | colvar bias setup generic core |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | FLUSH UPPER_WALLS ENERGY PRINT COMBINE DISTANCE METAD UNITS | colvar function bias setup generic |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | COORDINATION FLUSH UPPER_WALLS DUMPGRID HISTOGRAM WHOLEMOLECULES FIT_TO_TEMPLATE COM GROUP CONVERT_TO_FES PRINT MATHEVAL READ REWEIGHT_METAD ENDPLUMED WRAPAROUND POSITION METAD | vatom colvar bias function generic gridtools core |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | TORSION LOWER_WALLS UPPER_WALLS ENERGY VOLUME CELL PRINT MATHEVAL COMBINE ENDPLUMED METAD | function colvar generic bias |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | MOLINFO WHOLEMOLECULES GROUP EMMI BIASVALUE PRINT | isdb bias generic core |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | MOLINFO GROUP EMMI BIASVALUE PRINT | isdb bias generic core |
| 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 | OPES_METAD_EXPLORE GROUP BIASVALUE PRINT CUSTOM COORDINATION LOWER_WALLS LOAD CENTER | opes generic bias core colvar setup function vatom |
| 26.001 | Molecular simulations Alx riboswitch | bio | RNA, riboswitch | Giovanni Bussi | MOVINGRESTRAINT PRINT MATHEVAL ERMSD RESTRAINT DISTANCE MOLINFO | bias function colvar 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 | METAD WHOLEMOLECULES GROUP PRINT GYRATION COMBINE UPPER_WALLS COORDINATION MATHEVAL LOWER_WALLS DISTANCE CENTER | generic bias core colvar function vatom |
| 25.027 | Enhanced-sampling MD simulations of a protein-peptide complex integrating SAXS and XL-MS experimental information | bio | steered MD, metadynamics, SAXS, XL-MS, ensemble reconstruction | Mattia Bernetti | MOVINGRESTRAINT METAD WHOLEMOLECULES GROUP PRINT SAXS GYRATION UPPER_WALLS INCLUDE DISTANCE CENTER MOLINFO | generic bias core colvar isdb vatom |
| 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 CELL PRINT ENERGY BIASVALUE CUSTOM COMBINE UNITS COORDINATION POSITION MATHEVAL FLUSH INCLUDE TORSION LOAD DISTANCE | opes generic bias colvar setup function |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | STATS WHOLEMOLECULES GROUP METAINFERENCE PRINT ENSEMBLE ALPHABETA RDC FLUSH DISTANCE MOLINFO | multicolvar generic core colvar isdb function |
| 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 | OPES_METAD FIT_TO_TEMPLATE WHOLEMOLECULES FIXEDATOM GROUP PRINT CUSTOM PYTORCH_MODEL UPPER_WALLS COORDINATION LOWER_WALLS PATH RESTART TORSION DISTANCE CENTER | opes generic mapping bias core pytorch colvar setup function 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 | OPES_METAD WHOLEMOLECULES PRINT CUSTOM GYRATION COMBINE COORDINATION ALPHARMSD TORSION DISTANCE MOLINFO | opes generic secondarystructure colvar function |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | WHOLEMOLECULES GROUP BIASVALUE PRINT EMMIVOX ERMSD INCLUDE RESTRAINT MOLINFO | generic bias core colvar isdb |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | METAD FIXEDATOM PRINT UPPER_WALLS COMBINE DUMPMASSCHARGE RESTRAINT DISTANCE CENTER MOLINFO | generic bias colvar function 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 | METAD WHOLEMOLECULES PRINT BIASVALUE COMBINE COORDINATION ERMSD GHBFIX MOLINFO | bias function colvar generic |
| 23.030 | Data Driven Classification of Ligand Unbinding Pathways | bio | OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time | Dhiman Ray | FIT_TO_TEMPLATE BIASVALUE COMMITTOR LOWER_WALLS ENDPLUMED POSITION COM CENTER OPES_METAD OPES_METAD_EXPLORE WHOLEMOLECULES ENERGY DISTANCE WRAPAROUND MOLINFO COORDINATION UNITS FLUSH TORSION GROUP PRINT CUSTOM UPPER_WALLS MATHEVAL | opes generic bias core colvar setup function vatom |
| 23.029 | An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations | bio | SAXS, SANS, SAS, metainference, proteins, nucleic-acid | Federico Ballabio | STATS PRINT BIASVALUE SAXS GROUP RMSD CENTER UPPER_WALLS ENSEMBLE DISTANCE WRAPAROUND MOLINFO | generic bias core colvar isdb function vatom |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | WHOLEMOLECULES PRINT ENERGY OPES_EXPANDED ECV_UMBRELLAS_LINE ECV_MULTITHERMAL CONTACTMAP | opes colvar generic |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | OPES_METAD_EXPLORE PRINT PYTORCH_MODEL CUSTOM COORDINATION UNITS | opes generic pytorch colvar setup function |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | METAD WHOLEMOLECULES GROUP PRINT GYRATION UPPER_WALLS COORDINATION LOWER_WALLS FLUSH | bias core 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 | OPES_METAD PRINT ENERGY CUSTOM AROUND ENVIRONMENTSIMILARITY UPPER_WALLS HISTOGRAM DUMPGRID RESTART VOLUME | envsim opes generic bias volumes gridtools colvar setup function |
| 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 | ANGLE METAD WHOLEMOLECULES PRINT UPPER_WALLS COORDINATION ALPHABETA ALPHARMSD FLUSH TORSION DISTANCE MOLINFO | multicolvar generic bias secondarystructure colvar |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | OPES_METAD OPES_METAD_EXPLORE PRINT GROUP PYTORCH_MODEL CUSTOM UPPER_WALLS COORDINATION UNITS MATHEVAL LOWER_WALLS COM LOAD DISTANCE | opes generic bias core pytorch colvar setup function vatom |
| 22.001 | Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials | methods | enhanced sampling, variationally enhanced sampling, ves, metadynamics, bias representation, wavelets, adam | Benjamin Pampel | VES_LINEAR_EXPANSION BF_CUBIC_B_SPLINES BF_WAVELETS BF_GAUSSIANS POSITION VES_OUTPUT_BASISFUNCTIONS ENERGY OPT_ADAM INCLUDE DISTANCE METAD BF_LEGENDRE UNITS COORDINATION TD_UNIFORM FLUSH PRINT BF_CHEBYSHEV OPT_AVERAGED_SGD TD_WELLTEMPERED UPPER_WALLS | generic bias ves colvar setup |
| 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 | EMMI WHOLEMOLECULES GROUP BIASVALUE PRINT UPPER_WALLS RESTART COM DISTANCE MOLINFO | generic bias core setup isdb colvar vatom |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | METAD WHOLEMOLECULES GROUP PRINT SAXS CUSTOM GYRATION UPPER_WALLS ERMSD LOWER_WALLS INCLUDE MOLINFO | generic bias core colvar isdb function |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | WHOLEMOLECULES PRINT PBMETAD GYRATION COORDINATION ALPHABETA INCLUDE DIHCOR MOLINFO | bias multicolvar colvar generic |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | METAD PRINT GROUP COMBINE UPPER_WALLS UNITS RESTART ENDPLUMED FLUSH COORDINATIONNUMBER DISTANCES | generic multicolvar bias core setup function symfunc |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | METAD PRINT PATHMSD UPPER_WALLS UNITS LOWER_WALLS RESTART | bias colvar setup generic |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | COMBINE ANN COM POSITION RESTRAINT | bias annfunc colvar function vatom |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | PRINT ENERGY ENVIRONMENTSIMILARITY UNITS TORSION Q6 ENDPLUMED POSITION LOAD | envsim generic setup colvar symfunc |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | METAD CELL PRINT AROUND UPPER_WALLS UNITS LOWER_WALLS ENDPLUMED FCCUBIC | generic bias volumes colvar setup symfunc |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | OUTER_PRODUCT CONTACT_MATRIX DFSCLUSTERING METAD PRINT CLUSTER_DISTRIBUTION CUSTOM CLUSTER_NATOMS COORDINATIONNUMBER Q6 MATRIX_VECTOR_PRODUCT LOCAL_Q6 SMAC OUTPUT_CLUSTER DISTANCES CLUSTER_PROPERTIES MORE_THAN ONES | generic multicolvar bias adjmat matrixtools function symfunc clusters |
| 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 PRINT ENERGY UPPER_WALLS COM DISTANCE | bias vatom colvar generic |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | METAD WHOLEMOLECULES FUNNEL_PS PRINT RMSD FUNNEL UPPER_WALLS LOWER_WALLS COM DISTANCE | funnel generic bias colvar vatom |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | METAD WHOLEMOLECULES PRINT ENERGY GYRATION ALPHARMSD ENDPLUMED MOLINFO | bias secondarystructure colvar generic |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | METAD PRINT UPPER_WALLS COMMITTOR LOWER_WALLS TORSION DISTANCE CENTER | bias vatom colvar generic |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | METAD PRINT GYRATION RESTART ENDPLUMED COORDINATIONNUMBER DISTANCES | generic multicolvar bias colvar setup symfunc |