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 |
|---|---|---|---|---|---|---|
| 26.013 | 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 | PBMETAD PRINT WHOLEMOLECULES CONTACTMAP DUMPMASSCHARGE GROUP INCLUDE MOLINFO GYRATION COM COORDINATION ALPHARMSD DISTANCE | colvar core secondarystructure vatom bias generic |
| 26.002 | A Transferable and Robust Computational Framework for Class A GPCR Activation Free Energies | bio | OneOPES, GPCR, ADRB1, activation, euclidean path, microswitches, conformational changes, allostery | Valerio Rizzi | UPPER_WALLS VOLUME OPES_METAD_EXPLORE CENTER LOWER_WALLS PRINT PATH ECV_MULTITHERMAL RMSD DISTANCE GROUP OPES_EXPANDED CUSTOM PATHMSD COORDINATION ENERGY | function colvar mapping core opes vatom bias 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 | UPPER_WALLS CENTER LOWER_WALLS PRINT WHOLEMOLECULES METAD MATHEVAL GROUP COMBINE GYRATION COORDINATION DISTANCE | function colvar core vatom bias generic |
| 25.026 | Deciphering the Molecular Mechanisms of Startle Disease - the Role of the Asn46Lys Mutation in the Glycine Receptor | bio | metadynamics, glycine receptors, funnel metadynamics | Jacob Adam Clark | UPPER_WALLS FUNNEL LOWER_WALLS FUNNEL_PS PRINT METAD COM | funnel vatom bias generic |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | POSITION UPPER_WALLS OPES_METAD LOWER_WALLS PRINT WHOLEMOLECULES RMSD TORSION METAD DISTANCE GROUP MOLINFO PYTORCH_MODEL UNITS BIASVALUE CUSTOM ENDPLUMED ENERGY | setup function pytorch colvar core opes bias generic |
| 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 | UPDATE_IF READ VOLUME CENTER ENERGY PBMETAD PRINT WHOLEMOLECULES TORSION INCLUDE MOLINFO RESTART GYRATION DUMPATOMS DISTANCE | colvar generic vatom bias setup |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | OPES_METAD PRINT WHOLEMOLECULES TORSION DISTANCE MATHEVAL COMBINE GROUP COMMITTOR MOLINFO PYTORCH_MODEL CUSTOM ENDPLUMED ENERGY | function pytorch colvar core opes generic |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | UPPER_WALLS PRINT WHOLEMOLECULES DISTANCE METAD GROUP MOLINFO RESTART COM FUNCPATHGENERAL | function colvar core generic vatom bias setup |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | PRINT PUCKERING TORSION METAD RESTART MOLINFO | setup colvar bias 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 | UPPER_WALLS CENTER LOWER_WALLS PRINT GHBFIX METAD COMBINE GROUP MOLINFO BIASVALUE COORDINATION COM DEBUG DISTANCE | function colvar core vatom bias generic |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | UPPER_WALLS PRINT DFSCLUSTERING CLUSTER_PROPERTIES METAD CONTACT_MATRIX UNITS CLUSTER_NATOMS COORDINATIONNUMBER | adjmat clusters generic symfunc 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 | FLUSH SUM TRANSPOSE PRINT METAD MATHEVAL SELECT_COMPONENTS INCLUDE | function valtools matrixtools bias generic |
| 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 | UPPER_WALLS PRINT WHOLEMOLECULES GROUP INCLUDE EMMIVOX MOLINFO BIASVALUE WRAPAROUND DISTANCE | isdb colvar core bias generic |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | Q6 LOWER_WALLS PRINT METAD COMBINE GROUP MOVINGRESTRAINT LOCAL_Q6 MFILTER_MORE COORDINATIONNUMBER | function core symfunc bias multicolvar generic |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | LOAD PINES PBMETAD PRINT | pines generic bias setup |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | UPPER_WALLS PBMETAD PRINT GYRATION COM DISTANCE | colvar vatom bias generic |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | DRR UPPER_WALLS FLUSH LOWER_WALLS PRINT METAD BIASVALUE CUSTOM PATHMSD | function colvar drr bias generic |
| 23.000 | Atomistic simulations of RNA tetraloop folding via PTWTE-WTM | bio | parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding | Gül Zerze | UPPER_WALLS LOWER_WALLS PRINT WHOLEMOLECULES CONTACTMAP METAD ENERGY | colvar bias generic |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | PRINT TORSION METAD | colvar bias generic |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | UPPER_WALLS LOWER_WALLS PRINT WHOLEMOLECULES METAD PCAVARS | mapping bias generic |
| 22.035 | Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties | bio | intrinsically disordered proteins, parallel bias metadynamics, protein | Kresten Lindorff-Larsen | PBMETAD WHOLEMOLECULES TORSION MOLINFO GYRATION | colvar bias generic |
| 22.034 | Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods | materials | metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene | Matteo Salvalaglio | CELL UPPER_WALLS LOWER_WALLS DRMSD PRINT METAD MATHEVAL COMMITTOR CUSTOM | function generic bias colvar |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | READ DUMPGRID PRINT CONVERT_TO_FES PUCKERING TORSION METAD MOLINFO HISTOGRAM | colvar gridtools 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 | UPPER_WALLS OPES_METAD CENTER LOWER_WALLS PRINT WHOLEMOLECULES RMSD MATHEVAL GROUP COMMITTOR FIXEDATOM PYTORCH_MODEL COORDINATION FIT_TO_TEMPLATE CUSTOM DISTANCE | function pytorch colvar core opes vatom bias generic |
| 22.011 | Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck | methods | metadynamics, membrane permeation, protein folding | Shams Mehdi | ZANGLES UPPER_WALLS ALPHABETA LOWER_WALLS PRINT WHOLEMOLECULES TORSION METAD COMBINE MATHEVAL MOLINFO YANGLES CUSTOM COM XANGLES DISTANCE | function colvar vatom bias multicolvar generic |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | POSITION UPPER_WALLS OPES_METAD OPES_METAD_EXPLORE LOWER_WALLS PBMETAD PRINT ECV_MULTITHERMAL TORSION METAD OPES_EXPANDED UNITS BIASVALUE CUSTOM ENDPLUMED ECV_UMBRELLAS_FILE ENERGY | function colvar opes generic bias setup |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | PRINT CENTER DISTANCE | colvar vatom 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 | UPPER_WALLS ALPHABETA LOWER_WALLS PRINT WHOLEMOLECULES METAD GROUP GYRATION ENDPLUMED | colvar core bias multicolvar generic |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | FLUSH VOLUME CONTACTMAP INCLUDE MOLINFO DISTANCE OPES_METAD LOAD COMBINE GROUP ENERGY ENVIRONMENTSIMILARITY WHOLEMOLECULES RMSD OPES_EXPANDED UNITS PYTORCH_MODEL Q6 ECV_MULTITHERMAL PRINT TORSION ENDPLUMED | function pytorch colvar envsim core opes generic symfunc setup |
| 21.030 | Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains | bio | parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure | Jim Pfaendtner | ALPHABETA ENERGY PBMETAD PRINT TORSION METAD INCLUDE COORDINATION COM GYRATION DISTANCE | colvar vatom bias multicolvar generic |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | OPES_METAD ECV_MULTITHERMAL PRINT TORSION OPES_EXPANDED ECV_UMBRELLAS_LINE ENDPLUMED ENERGY | colvar generic opes |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | FLUSH CENTER PBMETAD PRINT WHOLEMOLECULES EEFSOLV GROUP MOLINFO BIASVALUE SAXS GYRATION METAINFERENCE ALPHARMSD | isdb colvar core secondarystructure vatom bias generic |
| 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 | UPPER_WALLS LOWER_WALLS LOAD WHOLEMOLECULES PRINT CONTACTMAP DISTANCE METAD MATHEVAL GROUP INCLUDE MOLINFO BIASVALUE COM CONSTANT PROJECTION_ON_AXIS FUNCPATHGENERAL | setup function colvar core vatom bias generic |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | UPPER_WALLS PRINT WHOLEMOLECULES RMSD TORSION METAD COMBINE RESTART MOLINFO DISTANCE | function colvar generic bias setup |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | FLUSH INCLUDE METAD | bias generic |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | POSITION RESTRAINT ANN COMBINE COM | function colvar vatom bias annfunc |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | CELL UPPER_WALLS AROUND LOWER_WALLS PRINT METAD FCCUBIC UNITS ENDPLUMED | setup volumes colvar symfunc bias generic |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | Q6 MATRIX_VECTOR_PRODUCT CLUSTER_DISTRIBUTION MORE_THAN DFSCLUSTERING OUTER_PRODUCT PRINT CLUSTER_PROPERTIES DISTANCES METAD SMAC LOCAL_Q6 CONTACT_MATRIX ONES CUSTOM CLUSTER_NATOMS OUTPUT_CLUSTER COORDINATIONNUMBER | adjmat clusters function matrixtools symfunc bias multicolvar generic |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | UPPER_WALLS LOWER_WALLS PRINT WHOLEMOLECULES METAD COM DISTANCE | colvar vatom bias generic |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | EXTERNAL METAD GROUP COORDINATION ENERGY | colvar bias core |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | UPPER_WALLS ALPHABETA CENTER RESTRAINT PBMETAD PRINT WHOLEMOLECULES DHENERGY DIHCOR TORSION GROUP STATS RDC MOLINFO ENSEMBLE METAINFERENCE ENDPLUMED DISTANCE | function isdb colvar core vatom bias multicolvar generic |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | PBMETAD PRINT WHOLEMOLECULES GROUP INCLUDE MOLINFO METAINFERENCE | core isdb bias generic |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | CS2BACKBONE PRINT WHOLEMOLECULES GROUP RDC MOLINFO METAINFERENCE | isdb core generic |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | ERMSD FLUSH UPPER_WALLS LOWER_WALLS RANDOM_EXCHANGES PRINT DISTANCES METAD COMBINE ANGLE INCLUDE MOLINFO DISTANCE | function colvar bias multicolvar generic |
| 26.016 | Cryo-EM ensemble of the PilQ secretin | bio | EMMIVox, cryo-EM, ensemble | Tatiana I. Morozova | EMMIVOX GROUP MOLINFO WHOLEMOLECULES BIASVALUE PRINT | core isdb generic bias |
| 25.030 | Committor Regularization | methods | metadynamics, enhanced sampling, mlcvs, committor, machine learning | Florian Dietrich | UNITS PRINT METAD MOVINGRESTRAINT | generic bias setup |
| 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 | FIXEDATOM DISTANCE COM CONVERT_TO_FES DUMPGRID METAD MOLINFO LOWER_WALLS HISTOGRAM UPPER_WALLS WHOLEMOLECULES REWEIGHT_BIAS PRINT | bias generic vatom colvar gridtools |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | ENERGY TORSION DISTANCE OPES_METAD CUSTOM GROUP LOAD COORDINATION COMBINE PRINT | function generic core colvar opes setup |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | SORT DISTANCE WHOLEMOLECULES PUCKERING POSITION GYRATION GROUP METAD MOLINFO CENTER LOWER_WALLS DISTANCES UPPER_WALLS COMBINE GHOST MATHEVAL PRINT | bias function generic multicolvar core vatom colvar |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | FLUSH TORSION RESTART METAD WHOLEMOLECULES PRINT | colvar generic bias setup |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | UNITS TORSION GROUP METAD PRINT | bias generic core colvar setup |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | ENERGY INCLUDE CONTACTMAP MOLINFO UPPER_WALLS WHOLEMOLECULES ECV_MULTITHERMAL OPES_EXPANDED PRINT | colvar opes generic bias |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | UNITS TORSION RESTART METAD PRINT | colvar generic bias setup |
| 23.031 | Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN | bio | RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites | Max Bonomi | FIT_TO_TEMPLATE POSITION GROUP MOLINFO SHADOW METAD WRAPAROUND CENTER DISTANCES UPPER_WALLS WHOLEMOLECULES PRINT | isdb bias multicolvar generic core vatom colvar |
| 23.030 | Data Driven Classification of Ligand Unbinding Pathways | bio | OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time | Dhiman Ray | UNITS DISTANCE COM GROUP CENTER WHOLEMOLECULES PRINT MATHEVAL OPES_METAD_EXPLORE TORSION OPES_METAD POSITION FLUSH CUSTOM FIT_TO_TEMPLATE MOLINFO ENDPLUMED COORDINATION UPPER_WALLS BIASVALUE ENERGY WRAPAROUND LOWER_WALLS COMMITTOR | bias function generic vatom core colvar opes setup |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | OPES_METAD_EXPLORE DISTANCE COM CUSTOM GROUP METAD CENTER LOWER_WALLS COORDINATION UPPER_WALLS WHOLEMOLECULES PRINT | bias function generic vatom core colvar opes |
| 23.010 | An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands | bio | GPCR, binding free energy, free energy surface | Timothy Clark | CONSTANT DISTANCE WHOLEMOLECULES METAD LOWER_WALLS UPPER_WALLS PRINT MATHEVAL BIASVALUE | colvar function generic bias |
| 23.009 | Deep Learning Collective Variables from Transition Path Ensemble | methods | TPI-Deep-TDA, Deep-TDA, Transition Path, OPES, OPES Flooding, Machine Learning, Protein folding, Ligand binding | Dhiman Ray | FIXEDATOM DISTANCE GROUP CENTER WHOLEMOLECULES PRINT MATHEVAL OPES_METAD INCLUDE CONTACTMAP ANGLE COMBINE CUSTOM FIT_TO_TEMPLATE MOLINFO ENDPLUMED COORDINATION PYTORCH_MODEL UPPER_WALLS ENERGY RMSD LOWER_WALLS COMMITTOR | bias function generic vatom core colvar opes pytorch |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | RMSD DISTANCE CONVERT_TO_FES DUMPGRID METAD MOLINFO HISTOGRAM REWEIGHT_METAD WHOLEMOLECULES READ MATHEVAL PRINT | bias function generic colvar gridtools |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | OPES_EXPANDED RESTART INCLUDE ECV_UMBRELLAS_LINE LOWER_WALLS UPPER_WALLS PRINT ENVIRONMENTSIMILARITY | bias generic opes envsim setup |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | ENERGY CONTACTMAP ECV_UMBRELLAS_LINE WHOLEMOLECULES ECV_MULTITHERMAL OPES_EXPANDED PRINT | colvar opes generic |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | TORSION RESTART ALPHABETA COM MOLINFO ANTIBETARMSD ALPHARMSD PBMETAD WHOLEMOLECULES PRINT | bias multicolvar generic secondarystructure vatom colvar setup |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | RMSD DISTANCE COM MOLINFO METAD COMMITTOR COMBINE WHOLEMOLECULES COORDINATIONNUMBER PRINT | bias function generic symfunc vatom colvar |
| 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 | FLUSH TORSION DISTANCE ALPHABETA ANGLE MOLINFO METAD ALPHARMSD COORDINATION UPPER_WALLS WHOLEMOLECULES PRINT | bias multicolvar generic secondarystructure colvar |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | UNITS DISTANCE INCLUDE CONTACTMAP RANDOM_EXCHANGES MOLINFO ANTIBETARMSD ALPHARMSD CENTER METAD COORDINATION PRINT | bias secondarystructure generic vatom colvar setup |
| 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 | ENERGY VES_LINEAR_EXPANSION OPES_EXPANDED RESTART VOLUME TD_UNIFORM Q6 ECV_UMBRELLAS_LINE ECV_MULTITHERMAL_MULTIBARIC OPT_AVERAGED_SGD UPPER_WALLS PRINT BF_LEGENDRE ENVIRONMENTSIMILARITY MATHEVAL | ves bias function generic symfunc colvar opes envsim setup |
| 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 |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | ENERGY FIXEDATOM DISTANCE OPES_METAD FIT_TO_TEMPLATE GROUP ANGLE CENTER ENDPLUMED COORDINATION PYTORCH_MODEL UPPER_WALLS WHOLEMOLECULES MATHEVAL PRINT | bias function generic vatom core colvar opes pytorch |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | RESTART DISTANCE GROUP CENTER DISTANCES COORDINATION WHOLEMOLECULES PRINT | multicolvar generic core vatom colvar setup |
| 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 | UNITS CUSTOM METAD DISTANCES COORDINATION PRINT | bias function multicolvar generic colvar setup |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_LOSS UNITS MAZE_OPTIMIZER_BIAS MAZE_SIMULATED_ANNEALING POSITION PRINT | colvar generic maze setup |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | ENERGY GYRATION METAD WHOLEMOLECULES PRINT | colvar generic bias |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | ENERGY UNITS FLUSH DISTANCE METAD UPPER_WALLS COMBINE PRINT | bias function generic colvar setup |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | TORSION DISTANCE COM GROUP PRINT RESTRAINT | bias generic vatom core colvar |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | TORSION DISTANCE EDS COMBINE RESTRAINT PRINT | eds bias function generic colvar |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | EMMI GROUP MOLINFO PRINT BIASVALUE | core isdb generic bias |
| 26.008 | Ensemble Dynamics | methods | State Exploration, Protein Folding, Drug Binding, Phase Transition | Florian M. Dietrich | DISTANCE POSITION CUSTOM BIASVALUE PRINT UNITS TORSION LOAD GROUP CELL OPES_METAD_EXPLORE | function generic setup core colvar opes bias |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | ABMD PATHMSD PRINT UNITS UPPER_WALLS ENDPLUMED | colvar generic setup bias |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | COMBINE ERMSD MOLINFO WHOLEMOLECULES METAD | colvar function generic bias |
| 24.025 | Correlating Enzymatic Reactivity for Different Substrates using Transferable Data-Driven Collective Variables | bio | enzymatic reactivity, k_cat, transfer learning, data-driven CVs, catalysis, ligand-binding modes, water, alpha-amylase, sugar, classical MD, OPES, machine learning, Deep TDA CV, path CV | Sudip Das | DISTANCE PATH RESTART OPES_METAD PRINT TORSION UPPER_WALLS CENTER FIXEDATOM PYTORCH_MODEL LOWER_WALLS GROUP WHOLEMOLECULES FIT_TO_TEMPLATE CUSTOM COORDINATION | function mapping generic setup pytorch core colvar opes bias vatom |
| 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 | ANGLE DISTANCE OPES_EXPANDED ECV_MULTITHERMAL PRINT TORSION UPPER_WALLS FIXEDATOM CENTER MATHEVAL LOWER_WALLS GROUP OPES_METAD_EXPLORE WHOLEMOLECULES ENERGY FIT_TO_TEMPLATE ENDPLUMED COORDINATION | function generic core colvar opes bias vatom |
| 24.019 | Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning | bio | OPES, machine learning, protein folding, adaptive sampling | Mingyuan Zhang | DISTANCE OPES_METAD COMBINE PRINT TORSION ALPHARMSD GYRATION MOLINFO WHOLEMOLECULES CUSTOM COORDINATION | secondarystructure function generic colvar opes |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | INCLUDE CONTACTMAP CONSTANT ECV_MULTITHERMAL METAD LOWER_WALLS WHOLEMOLECULES WRAPAROUND RESTART BIASVALUE PRINT COM MOLINFO ENERGY OPES_METAD_EXPLORE COORDINATION PROJECTION_ON_AXIS RMSD OPES_EXPANDED UPPER_WALLS TORSION MATHEVAL GROUP CUSTOM | function generic setup core colvar opes bias vatom |
| 24.013 | Estimating Free Energy Surfaces and their Convergence from multiple, independent static and history-dependent biased molecular-dynamics simulations with Mean Force Integration | methods | Mean Force Integration, Convergence, FES, Umbrella Sampling | Matteo Salvalaglio | COMMITTOR DISTANCE RESTART BIASVALUE PRINT TORSION FLUSH RESTRAINT MATHEVAL MOLINFO COORDINATIONNUMBER ENERGY METAD | function generic setup colvar symfunc bias |
| 23.045 | Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state | bio | Path CVs Metadynamics, GPCRs activation transition | Vittorio Limongelli | DISTANCE INCLUDE CONTACTMAP PATHMSD PRINT UPPER_WALLS LOWER_WALLS ALPHARMSD MOLINFO METAD FUNCPATHMSD | secondarystructure function generic colvar bias |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | DISTANCE PRINT UPPER_WALLS COM LOWER_WALLS GYRATION MOLINFO PBMETAD | colvar generic vatom bias |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | POSITION COMBINE PRINT ALPHARMSD FIT_TO_TEMPLATE MOLINFO WHOLEMOLECULES METAD ANN | secondarystructure function generic colvar bias annfunc |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | AROUND CLUSTER_DISTRIBUTION DENSITY LOCAL_AVERAGE Q3 PRINT UNITS DUMPGRID HISTOGRAM CONTACT_MATRIX FIXEDATOM CLUSTER_NATOMS DFSCLUSTERING RESTRAINT GROUP LOAD COORDINATIONNUMBER LOCAL_Q3 | volumes gridtools adjmat generic setup core symfunc bias clusters vatom |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | DISTANCE CONSTANT BIASVALUE PRINT MATHEVAL ANGLE WHOLEMOLECULES PBMETAD | colvar function generic bias |
| 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 TORSION METAD | colvar generic bias |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | WHOLEMOLECULES PRINT TORSION | colvar generic |
| 22.027 | Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain | Max Bonomi | PRINT RMSD | 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 | DISTANCE PATHMSD PRINT UPPER_WALLS COM LOWER_WALLS FUNNEL_PS WHOLEMOLECULES FUNNEL METAD | generic funnel colvar bias vatom |
| 22.012 | Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT | bio | contact maps, protein-protein interactions | Isabell-Louise Grothaus | CENTER CONTACTMAP DISTANCE PRINT | colvar generic vatom |
| 22.008 | Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters | materials | Well tempered metadynamics, ab-initio, ase | Daniel Sucerquia | DISTANCE COMBINE UNITS UPPER_WALLS FLUSH COM LOWER_WALLS GYRATION COORDINATIONNUMBER METAD COORDINATION | function generic setup colvar symfunc bias vatom |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | COMMITTOR DISTANCE PRINT TORSION CENTER COORDINATIONNUMBER METAD ENDPLUMED | generic colvar symfunc bias vatom |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | KDE DISTANCE TORSIONS PRINT COM MATHEVAL | function gridtools generic colvar multicolvar vatom |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | INCLUDE PRINT UPPER_WALLS ERMSD GYRATION LOWER_WALLS GROUP MOLINFO WHOLEMOLECULES SAXS METAD CUSTOM | isdb function generic core colvar bias |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | VOLUME CELL PRINT UPPER_WALLS LOWER_WALLS MATHEVAL ENERGY METAD | colvar function generic bias |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | BIASVALUE GROUP PRINT LOAD EMMIVOX MOLINFO WHOLEMOLECULES DUMPATOMS | isdb generic setup core bias |
| 20.010 | Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations | materials | water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling | Pablo Piaggi | VOLUME VES_LINEAR_EXPANSION RESTART TD_WELLTEMPERED ENVIRONMENTSIMILARITY BF_LEGENDRE Q6 UPPER_WALLS PRINT MATHEVAL OPT_AVERAGED_SGD OPT_DUMMY | function ves generic setup envsim colvar symfunc bias |
| 20.002 | Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study | bio | Metadynamics, path CVs | Riccardo Ocello | RESTART PATHMSD PRINT UPPER_WALLS GROUP MOLINFO WHOLEMOLECULES METAD | generic setup core colvar bias |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | DISTANCES RESTART COMBINE PRINT UNITS UPPER_WALLS FLUSH GROUP COORDINATIONNUMBER METAD ENDPLUMED | function generic setup core symfunc bias multicolvar |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | DISTANCE VES_LINEAR_EXPANSION EXTERNAL TD_GRID TD_WELLTEMPERED COMBINE PRINT UPPER_WALLS UNITS FLUSH DUMPGRID HISTOGRAM BF_CHEBYSHEV OPT_AVERAGED_SGD LOWER_WALLS ANGLE CONVERT_TO_FES COORDINATION | function ves gridtools generic setup colvar bias |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | DISTANCE PRINT UPPER_WALLS COM GYRATION MOLINFO ENERGY METAD | colvar generic vatom bias |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | DISTANCE RESTRAINT LOWER_WALLS WHOLEMOLECULES ENDPLUMED COORDINATION | colvar generic bias |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | RANDOM_EXCHANGES INCLUDE PRINT TORSION METAD | colvar generic bias |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | PRINT TORSION MATHEVAL METAD ENDPLUMED | colvar function generic bias |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | PRINT UPPER_WALLS ALPHABETA GYRATION LOWER_WALLS GROUP MOLINFO WHOLEMOLECULES METAD | generic core colvar bias multicolvar |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | PRINT ALPHARMSD GYRATION MOLINFO WHOLEMOLECULES ENERGY METAD ENDPLUMED | secondarystructure colvar generic bias |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | COMMITTOR COMBINE PRINT ALPHABETA FLUSH MOLINFO METAD | bias function generic multicolvar |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | CONSTANT BIASVALUE PRINT TORSION MATHEVAL WHOLEMOLECULES METAD | colvar function generic bias |
| 26.014 | Dissociation free energy (DFE) calculationsfor GPR15L–polySia | bio | metadynamics, protein-carbohydrate interaction | Davide Luciano and Gaston Courtade | METAD COM GROUP UPPER_WALLS DISTANCE PRINT | bias colvar vatom core generic |
| 26.010 | Solvation-Mediated Ammonia Synthesis in a Nanoheterogeneous Liquid Alloy | materials | OPES, Catalysis, Ammonia Synthesis | Axel Tosello Gardini | DISTANCES FLUSH COORDINATION INCLUDE GROUP COORDINATIONNUMBER UPPER_WALLS OPES_METAD DISTANCE UNITS OPES_METAD_EXPLORE CUSTOM PRINT | multicolvar bias symfunc setup function colvar core generic opes |
| 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 | COM COORDINATION COMMITTOR OPES_METAD DISTANCE CUSTOM ENDPLUMED METAD TORSION GROUP MATHEVAL WHOLEMOLECULES PRINT CENTER WRAPAROUND RMSD LOWER_WALLS UPPER_WALLS FUNNEL FUNNEL_PS | bias function colvar vatom core generic opes funnel |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | STATS METAINFERENCE FLUSH SAXS CENTER UPPER_WALLS DISTANCE GYRATION ENSEMBLE TORSION WHOLEMOLECULES PBMETAD PRINT MOLINFO | isdb bias function colvar vatom generic |
| 25.012 | A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis | bio | enzyme catalysis, transition state, structure-activity relationship, free energy surface, reaction mechanism, water, alpha-amylase, sugar, QM/MM MD, OPES, committor function, machine learning | Sudip Das | FLUSH COMBINE BIASVALUE LOAD INCLUDE ENERGY COORDINATION OPES_METAD CUSTOM UNITS DISTANCE MATHEVAL TORSION CELL POSITION PRINT | bias setup function colvar generic opes |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | METAINFERENCE STATS ALPHABETA FLUSH GROUP RDC DISTANCE ENSEMBLE WHOLEMOLECULES PRINT MOLINFO | isdb multicolvar function colvar core generic |
| 24.020 | Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics | bio | LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning | Ziyue Zou, Dedi Wang, Pratyush Tiwary | METAD COMMITTOR LOAD GROUP TORSION PRINT | bias setup colvar core 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 GROUP COORDINATIONNUMBER UPPER_WALLS OPES_METAD DISTANCE UNITS FIXEDATOM ZDISTANCES PRINT | multicolvar bias symfunc setup colvar vatom core generic opes |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | COMBINE METAD DISTANCE UNITS WHOLEMOLECULES PRINT | bias setup function colvar generic |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | METAD LOAD INCLUDE CENTER COORDINATIONNUMBER GROUP PRINT | bias setup symfunc vatom core generic |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | RESTRAINT COM COORDINATION INCLUDE GYRATION TORSION WHOLEMOLECULES PBMETAD PRINT | colvar vatom generic bias |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | PYTORCH_MODEL COORDINATION CUSTOM UNITS OPES_METAD_EXPLORE PRINT | setup function colvar pytorch generic opes |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | FLUSH METAD COMBINE BIASVALUE LOAD COORDINATION GROUP GHBFIX UPPER_WALLS CUSTOM PRINT MOLINFO | bias setup function colvar core generic |
| 22.021 | Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn Løland Bore | INCLUDE LOWER_WALLS UPPER_WALLS ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY OPES_EXPANDED PRINT | envsim generic opes bias |
| 22.020 | Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA | bio | RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics | Weiwei He | METAD COM GROUP DISTANCE TORSION WHOLEMOLECULES PRINT | bias colvar vatom core generic |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | DISTANCES METAD COMBINE COM DUMPGRID INCLUDE GROUP CONVERT_TO_FES GYRATION HISTOGRAM REWEIGHT_BIAS PRINT | gridtools multicolvar bias function colvar vatom core generic |
| 21.043 | Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes | chemistry | well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability | Huixia Lu | METAD FIT_TO_TEMPLATE TORSION FIXEDATOM PRINT | colvar vatom generic bias |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | METAD ENERGY INCLUDE CONTACTMAP LOWER_WALLS UPPER_WALLS DISTANCE MATHEVAL WHOLEMOLECULES ALPHARMSD PRINT MOLINFO | bias function colvar generic secondarystructure |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | METAD PATHMSD COM UPPER_WALLS DISTANCE UNITS WHOLEMOLECULES PRINT | bias setup colvar vatom generic |
| 20.030 | Converging experimental and computational views of the knotting mechanism of the smallest knotted protein | bio | phi-values, transition state, knotted proteins | Cristina Paissoni | STATS COMBINE RESTRAINT COORDINATION WHOLEMOLECULES PRINT MOLINFO | colvar generic bias function |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | STATS RESTRAINT BIASVALUE SAXS INCLUDE CENTER GROUP DISTANCE ENSEMBLE WHOLEMOLECULES PRINT MOLINFO | isdb bias function colvar vatom core generic |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | DISTANCES COMBINE LOAD ENERGY GROUP UPPER_WALLS LOWER_WALLS DISTANCE UNITS TORSION PRINT | multicolvar bias setup function colvar core 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 | STATS RESTRAINT COORDINATION WHOLEMOLECULES PRINT MOLINFO | colvar generic bias function |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | MOLINFO COORDINATION INCLUDE DIHCOR GYRATION WHOLEMOLECULES PBMETAD PRINT ALPHABETA | colvar multicolvar generic bias |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | STATS METAINFERENCE MOLINFO FLUSH SAXS CENTER DISTANCE GYRATION ENSEMBLE TORSION WHOLEMOLECULES PBMETAD PRINT ALPHABETA | isdb multicolvar bias function colvar vatom generic |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | METAD BIASVALUE COMMITTOR DUMPGRID CONVERT_TO_FES REWEIGHT_METAD DISTANCE MATHEVAL TORSION HISTOGRAM REWEIGHT_BIAS EXTERNAL READ PRINT | gridtools bias function colvar generic |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | ENDPLUMED INCLUDE CENTER GROUP DISTANCE PRINT | colvar vatom generic core |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | METAD COM CENTER GROUP LOWER_WALLS UPPER_WALLS DISTANCE RESTART PRINT | bias setup colvar vatom core generic |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | DISTANCE_FROM_CONTOUR METAD COMBINE DUMPGRID CONVERT_TO_FES UPPER_WALLS HISTOGRAM REWEIGHT_BIAS RESTART READ PRINT | gridtools bias setup contour function generic |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | DISTANCES FLUSH METAD UPPER_WALLS PATH RESTART PRINT | multicolvar bias setup mapping generic |
| 26.012 | Buprenorphine Restricts the Conformational Landscape of the μ-Opioid Receptor | bio | OneOPES, GPCR, MOR, activation, euclidean path, conformational changes, allostery | Simone Aureli | CUSTOM RMSD PATH ECV_MULTITHERMAL COORDINATION GROUP PRINT UPPER_WALLS DISTANCE CENTER OPES_EXPANDED OPES_METAD_EXPLORE ENERGY VOLUME | generic opes colvar core mapping vatom function bias |
| 26.006 | Metadynamics simulations of buried phosphorylation sites and proline isomerisation | bio | metadynamics | Julian Streit | METAD MOLINFO WHOLEMOLECULES TORSION COORDINATION PRINT | generic colvar bias |
| 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 METAD PYTORCH_MODEL RMSD FUNNEL_PS WRAPAROUND WHOLEMOLECULES COM MATHEVAL LOWER_WALLS COORDINATION GROUP PRINT UPPER_WALLS DISTANCE ENERGY | generic colvar pytorch core funnel vatom function bias |
| 25.017 | Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity | bio | EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase | Samuel Hoff | EMMIVOX BIASVALUE MOLINFO WHOLEMOLECULES GROUP PRINT | isdb core bias generic |
| 25.015 | Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY | materials | Molecular crystal, Force Field, Collective Variable | Pradip Si and Omar Valsson | DISTANCES DUMPMULTICOLVAR PRINT SMAC TORSIONS | generic multicolvar symfunc |
| 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 | BIASVALUE PBMETAD RMSD MOLINFO WHOLEMOLECULES COM PARABETARMSD COORDINATION GROUP PRINT UPPER_WALLS DISTANCE CENTER DUMPMASSCHARGE DUMPATOMS EMMI ALPHARMSD | generic colvar secondarystructure isdb core vatom bias |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | METAD COMMITTOR READ HISTOGRAM COORDINATION GROUP PRINT ENDPLUMED DUMPGRID CONVERT_TO_FES | generic colvar core gridtools bias |
| 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 | BIASVALUE METAD MOLINFO WHOLEMOLECULES COMBINE ERMSD GHBFIX COORDINATION PRINT | generic colvar function bias |
| 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 | METAD RMSD MOLINFO READ WHOLEMOLECULES MATHEVAL HISTOGRAM REWEIGHT_METAD PRINT DISTANCE DUMPGRID CONVERT_TO_FES | generic colvar gridtools function bias |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | METAD WHOLEMOLECULES COM TORSION COMBINE PRINT UPPER_WALLS DISTANCE FLUSH | generic colvar vatom function bias |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | METAD MOLINFO TORSION ECV_MULTITHERMAL OPES_EXPANDED PRINT DISTANCE ENDPLUMED OPES_METAD_EXPLORE ENERGY | generic opes colvar bias |
| 23.004 | Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point | chemistry | water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential | Pablo Piaggi | ECV_UMBRELLAS_LINE HISTOGRAM LOWER_WALLS OPES_EXPANDED PRINT UPPER_WALLS ENVIRONMENTSIMILARITY DUMPGRID RESTART | generic opes bias gridtools setup envsim |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | METAD WHOLEMOLECULES COM MOVINGRESTRAINT LOWER_WALLS PRINT UPPER_WALLS DISTANCE ANGLE | generic vatom colvar bias |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | VOLUME CUSTOM BIASVALUE UNITS COMMITTOR ANN HISTOGRAM MOVINGRESTRAINT COORDINATIONNUMBER PRINT UPPER_WALLS RESTRAINT DUMPGRID REWEIGHT_BIAS FLUSH LOAD CONVERT_TO_FES | generic colvar symfunc gridtools setup annfunc function bias |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | RMSD PRINT | generic colvar |
| 22.001 | 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 | COORDINATION BF_LEGENDRE METAD BF_GAUSSIANS INCLUDE VES_OUTPUT_BASISFUNCTIONS BF_CHEBYSHEV UPPER_WALLS OPT_ADAM FLUSH BF_WAVELETS UNITS TD_WELLTEMPERED OPT_AVERAGED_SGD PRINT DISTANCE BF_CUBIC_B_SPLINES ENERGY VES_LINEAR_EXPANSION TD_UNIFORM POSITION | generic colvar ves setup bias |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | METAD LOCAL_Q6 DFSCLUSTERING CLUSTER_DISTRIBUTION HISTOGRAM INSPHERE COMBINE GROUP COORDINATIONNUMBER PRINT Q6 DUMPGRID CLUSTER_NATOMS MFILTER_MORE CONTACT_MATRIX FIXEDATOM | generic function symfunc core multicolvar gridtools adjmat clusters vatom volumes 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 | CUSTOM METAD COMBINE COORDINATION PRINT ENDPLUMED VOLUME | generic colvar function bias |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | GROUP PRINT DISTANCE RESTRAINT FIXEDATOM LOAD | generic colvar core setup vatom bias |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | METAD CONSTANT INCLUDE COMBINE MOVINGRESTRAINT PRINT UPPER_WALLS RESTRAINT | generic function bias |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | METAD UNITS WHOLEMOLECULES COM LOWER_WALLS PRINT UPPER_WALLS DISTANCE | generic colvar setup vatom bias |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | OPES_METAD CONSTANT COMBINE RESTRAINT METAD BF_CHEBYSHEV UPPER_WALLS FLUSH LOAD CONVERT_TO_FES UNITS TD_WELLTEMPERED MOVINGRESTRAINT OPT_AVERAGED_SGD COORDINATIONNUMBER PRINT REWEIGHT_METAD DISTANCE DUMPGRID VES_LINEAR_EXPANSION CUSTOM BIASVALUE ANN HISTOGRAM REWEIGHT_BIAS | generic opes colvar symfunc ves gridtools setup annfunc function bias |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | ENERGY UNITS BIASVALUE FISST MATHEVAL GROUP PRINT DISTANCE RESTRAINT GYRATION | generic fisst colvar core setup function bias |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | METAD INCLUDE GROUP PRINT CENTER UPPER_WALLS VOLUME LOAD | generic colvar core setup vatom bias |
| 20.005 | Muscarinic M2 receptor/ligand Frequency-Adaptive Metadynamics and QM/MM calculations | bio | Frequency-adaptive metadynamics, multiple-walkers metadynamics, well-tempered metadynamics, GPCR, receptor, Adiabatic Bias MD | Riccardo Capelli | READ COMBINE LOWER_WALLS METAD MOLINFO UPPER_WALLS FUNCPATHMSD ENDPLUMED CONTACTMAP FLUSH CONVERT_TO_FES WHOLEMOLECULES COM REWEIGHT_METAD PRINT DISTANCE DUMPGRID HISTOGRAM ABMD | generic colvar gridtools vatom function bias |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | METAD UNITS COMBINE GROUP COORDINATIONNUMBER PRINT ENDPLUMED EXTERNAL FLUSH RESTART | generic symfunc core setup function bias |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | METAD BIASVALUE CONSTANT WHOLEMOLECULES COM MATHEVAL LOWER_WALLS PRINT UPPER_WALLS DISTANCE | generic colvar vatom function bias |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | BIASVALUE PBMETAD MOLINFO WHOLEMOLECULES LOWER_WALLS GROUP ANTIBETARMSD ALPHABETA UPPER_WALLS PRINT ENDPLUMED CS2BACKBONE FLUSH RESTART | generic secondarystructure isdb core multicolvar setup bias |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | METAD PIV LOWER_WALLS PRINT UPPER_WALLS FUNCPATHMSD CELL | generic colvar piv function bias |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | LOCAL_Q6 COMMITTOR CLUSTER_WITHSURFACE DFSCLUSTERING Q6 OUTPUT_CLUSTER ENDPLUMED CLUSTER_NATOMS MFILTER_MORE CONTACT_MATRIX FLUSH | generic symfunc multicolvar adjmat clusters |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | BIASVALUE MOLINFO WHOLEMOLECULES GROUP PRINT EMMI | generic core bias isdb |
| 26.015 | Ensemble Dynamics | methods | State Exploration, Protein Folding, Drug Binding, Phase Transition | Florian M. Dietrich | BIASVALUE PRINT GROUP LOAD OPES_METAD_EXPLORE DISTANCE CUSTOM CELL TORSION UNITS POSITION | setup core opes bias colvar generic function |
| 26.009 | Exploring the Conformational Landscape of HIV-1 TAR RNA by PT-WTE | bio | RNA, PT-WTE, HIV-1 TAR | Stefano Bosio | METAD PRINT GROUP WHOLEMOLECULES MOLINFO ENERGY | colvar generic bias core |
| 26.000 | OPES simulations of disordered proteins | bio | OPES, IDPs | Julian Streit | PRINT RESTART ECV_MULTITHERMAL OPES_EXPANDED ENERGY | opes generic colvar setup |
| 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 | METAD PRINT UPPER_WALLS COM GROUP FLUSH ANGLE DISTANCE COMBINE LOWER_WALLS FIXEDATOM COORDINATION COORDINATIONNUMBER RESTRAINT UNITS DISTANCES | vatom multicolvar setup core bias symfunc colvar generic function |
| 24.035 | Data efficient machine learning potentials for modeling catalytic reactivity via active learning and enhanced sampling | chemistry | opes, catalysis, ammonia, machine learning potentials | Luigi Bonati | OPES_METAD PRINT UPPER_WALLS GROUP RESTART DISTANCE CUSTOM LOWER_WALLS COORDINATION COMMITTOR UNITS | setup core opes bias colvar generic function |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | PRINT RESTRAINT UNITS POSITION | setup generic colvar bias |
| 24.021 | Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state | chemistry | ion pairing, caco3, opes, proton transfer, crystallization | Pablo Piaggi | OPES_METAD PRINT UPPER_WALLS DISTANCE COORDINATION ENERGY | opes generic colvar bias |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | MOVINGRESTRAINT PRINT COM ALPHABETA DISTANCE WHOLEMOLECULES INCLUDE COORDINATION TORSION GYRATION | vatom multicolvar bias colvar 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 | RMSD METAD PRINT DISTANCE WHOLEMOLECULES MOLINFO MATHEVAL | bias generic colvar function |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | PRINT UPPER_WALLS COM PBMETAD DISTANCE MOLINFO GYRATION | colvar vatom generic bias |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | RMSD DISTANCE PRINT | generic colvar |
| 21.015 | Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin | bio | metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module | Gaston Courtade | METAD PRINT MATHEVAL RESTART WHOLEMOLECULES COORDINATION CENTER RESTRAINT REWEIGHT_BIAS POSITION | vatom setup bias colvar generic function |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | METAD REWEIGHT_METAD PRINT MOVINGRESTRAINT UPPER_WALLS CONVERT_TO_FES FLUSH LOAD COMMITTOR COORDINATIONNUMBER HISTOGRAM UNITS DUMPGRID | setup gridtools bias symfunc generic |
| 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 METAD DISTANCE PRINT | bias generic colvar |
| 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 | PRINT WHOLEMOLECULES DIHCOR COORDINATION METAINFERENCE ANTIBETARMSD STATS FLUSH COMBINE CS2BACKBONE INCLUDE ENDPLUMED PARABETARMSD GROUP PBMETAD ENSEMBLE MOLINFO ALPHARMSD GYRATION | multicolvar core secondarystructure bias colvar isdb generic function |
| 19.041 | Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces | bio | metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption | Jim Pfaendtner | METAD PRINT UPPER_WALLS COM DISTANCE ENERGY | colvar vatom generic bias |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | METAD PRINT UPPER_WALLS DISTANCE LOWER_WALLS TORSION CENTER COMMITTOR | colvar vatom generic bias |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 25.023 | Molecular simulations of Tau-protein oligomers | bio | metadynamics, proteins, aggregation | Giovanni Bussi | HISTOGRAM RESTART RESTRAINT CONTACTMAP DUMPGRID REWEIGHT_BIAS FLUSH PRINT METAD CONVERT_TO_FES CUSTOM RMSD | bias setup gridtools function colvar generic |
| 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 | WHOLEMOLECULES OPES_METAD_EXPLORE ENERGY FIT_TO_TEMPLATE MATHEVAL DISTANCE COORDINATION ANGLE PRINT CENTER GROUP UPPER_WALLS FIXEDATOM | core vatom bias function opes colvar generic |
| 25.016 | Advancing in silico drug design with Bayesian refinement of AlphaFold models | bio | bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment | Samiran Sen | PRINT GROUP BAIES BIASVALUE | core bias isdb generic |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | RESTRAINT GYRATION DISTANCE PRINT PYTORCH_MODEL | bias colvar pytorch generic |
| 25.004 | Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride | chemistry | OPES, OPES flooding, Catalysis, Ammonia Synthesis | Axel Tosello Gardini | UNITS COMMITTOR DISTANCE ZDISTANCES UPPER_WALLS DISTANCES PRINT FLUSH COORDINATIONNUMBER GROUP CUSTOM FIXEDATOM OPES_METAD | core bias vatom symfunc setup function opes multicolvar colvar generic |
| 24.036 | Leveraging cryptic ligand envelopes through enhanced molecular simulations | bio | HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope | Francesco Colizzi | HISTOGRAM DUMPGRID WHOLEMOLECULES DISTANCE COORDINATION TORSION PRINT ANGLE CONVERT_TO_FES GROUP | core colvar gridtools 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 WHOLEMOLECULES PARABETARMSD GYRATION DISTANCE ALPHARMSD ANTIBETARMSD MOLINFO COORDINATION TORSION FLUSH PBMETAD PRINT ENDPLUMED GROUP COMBINE INCLUDE | core bias function multicolvar secondarystructure colvar generic |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | UNITS MATHEVAL COORDINATION PRINT GROUP LOAD TORSION POSITION INCLUDE RMSD WHOLEMOLECULES LOWER_WALLS UPPER_WALLS CUSTOM BIASVALUE ENERGY DISTANCE CELL MOLINFO ENDPLUMED | core bias setup function colvar generic |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | MATHEVAL COORDINATION PRINT CONVERT_TO_FES PATH GROUP FIXEDATOM COM FLUSH METAD INCLUDE RMSD WHOLEMOLECULES COMMITTOR READ UPPER_WALLS FIT_TO_TEMPLATE CONTACTMAP REWEIGHT_METAD HISTOGRAM DUMPGRID DISTANCE MOLINFO ENDPLUMED WRAPAROUND | core mapping vatom bias gridtools function colvar generic |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | RESTART LOAD PRINT METAD GROUP INCLUDE | core setup bias generic |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | MATHEVAL DISTANCE CUSTOM TORSION PRINT METAD CENTER UPPER_WALLS FIXEDATOM | vatom bias function colvar generic |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | CONTACTMAP COM DISTANCE ALPHARMSD MOLINFO ANGLE PRINT METAD DUMPFORCES | vatom bias secondarystructure colvar generic |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | UNITS PRINT CONSTANT GROUP OPES_METAD TORSION POSITION COMBINE INCLUDE RMSD WHOLEMOLECULES COMMITTOR CUSTOM BIASVALUE ENERGY CONTACTMAP DISTANCE MOLINFO ENDPLUMED PYTORCH_MODEL | core bias setup pytorch function opes colvar generic |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | ENERGY LOAD PRINT VOLUME METAD CENTER COORDINATIONNUMBER GROUP COMBINE INCLUDE | core vatom bias symfunc setup function colvar generic |
| 21.034 | Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics | bio | reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics | Dongdong Wang | PBMETAD TORSION PRINT ENDPLUMED METAD RANDOM_EXCHANGES INCLUDE | 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 | WHOLEMOLECULES UNITS COORDINATION PBMETAD GROUP | core bias setup colvar generic |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | ENERGY RESTART MOLINFO TORSION PRINT FLUSH EXTERNAL | setup bias colvar generic |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | ENERGY GYRATION COM LOWER_WALLS DISTANCE MOLINFO PBMETAD PRINT UPPER_WALLS | bias vatom colvar generic |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | MATHEVAL COORDINATION PRINT CONVERT_TO_FES GROUP FIXEDATOM COM POSITION FLUSH METAD RMSD WHOLEMOLECULES READ UPPER_WALLS REWEIGHT_METAD HISTOGRAM DUMPGRID DISTANCE ENDPLUMED | core vatom bias gridtools function colvar generic |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | WHOLEMOLECULES RESTART CONTACTMAP REWEIGHT_BIAS ALPHARMSD ALPHABETA MOLINFO PBMETAD PRINT METAD GROUP | core bias setup multicolvar secondarystructure colvar generic |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | MATHEVAL LOWER_WALLS LOAD FLUSH PRINT PYTORCH_MODEL GROUP UPPER_WALLS OPES_METAD | core bias setup pytorch function opes generic |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | HISTOGRAM DUMPGRID WHOLEMOLECULES MOLINFO EMMI PRINT CONVERT_TO_FES GROUP READ DISTANCES BIASVALUE RMSD | core bias isdb gridtools multicolvar colvar generic |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | TORSION PRINT METAD | bias colvar generic |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | UNITS MATHEVAL PRINT ECV_UMBRELLAS_LINE LOAD ECV_MULTITHERMAL TORSION POSITION VOLUME RMSD WHOLEMOLECULES ENVIRONMENTSIMILARITY ECV_LINEAR OPES_EXPANDED ECV_MULTITHERMAL_MULTIBARIC UPPER_WALLS CUSTOM ENERGY Q6 MOLINFO ENDPLUMED | bias envsim symfunc setup function opes colvar generic |
| 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 | WHOLEMOLECULES LOWER_WALLS ANTIBETARMSD ALPHABETA MOLINFO PBMETAD PRINT FLUSH ENDPLUMED CS2BACKBONE GROUP UPPER_WALLS BIASVALUE | core bias isdb multicolvar secondarystructure generic |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | UNITS TORSION PRINT ENDPLUMED METAD POSITION EXTERNAL OPES_METAD | bias setup opes colvar generic |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | ENERGY ENVIRONMENTSIMILARITY UNITS Q6 LOAD TORSION POSITION PRINT ENDPLUMED | envsim symfunc setup colvar generic |
| 19.045 | Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water | materials | metadynamics, well-tempered, multiple walkers, LAMMPS | Marco De La Pierre | RESTART UNITS LOWER_WALLS COORDINATION POSITION PRINT METAD FLUSH GROUP UPPER_WALLS | core bias setup colvar generic |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | RESTART UNITS DISTANCE PRINT FLUSH METAD DISTANCES UPPER_WALLS COMBINE | bias setup function multicolvar colvar generic |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | WHOLEMOLECULES GYRATION TORSION PRINT METAD | bias colvar generic |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | RESTART GYRATION PRINT ENDPLUMED METAD COORDINATIONNUMBER DISTANCES | bias symfunc setup multicolvar colvar generic |
| 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 | CUSTOM COORDINATION LOAD CENTER OPES_METAD_EXPLORE GROUP BIASVALUE LOWER_WALLS PRINT | setup function generic core vatom opes colvar bias |
| 26.005 | Cryptic pocket discovery in Alzheimer disease risk proteins BIN1, PICALM, and CD2AP via well-tempered metadynamics | methods | cryptic pockets, Alzheimer disease, BIN1, PICALM, CD2AP, well-tempered metadynamics, endocytosis, clathrin-mediated trafficking, virtual screening | Cagrı Ozkurt | METAD DISTANCE ANGLE PRINT WHOLEMOLECULES | generic colvar bias |
| 26.001 | Molecular simulations Alx riboswitch | bio | RNA, riboswitch | Giovanni Bussi | MATHEVAL ERMSD DISTANCE MOVINGRESTRAINT MOLINFO RESTRAINT PRINT | generic colvar function bias |
| 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 | PATHMSD OPES_EXPANDED RMSD CUSTOM DISTANCE UPPER_WALLS COORDINATION ECV_MULTITHERMAL CENTER ENERGY OPES_METAD_EXPLORE GROUP DISTANCES LOWER_WALLS GHOST PRINT | function generic multicolvar core vatom opes colvar bias |
| 25.014 | Atomic resolution ensembles of intrinsically disordered proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | GROUP BIASVALUE BAIES PRINT | generic isdb core bias |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | MATHEVAL UPPER_WALLS DISTANCE RESTART MULTI_RMSD UNITS LOWER_WALLS PBMETAD PRINT | setup function generic colvar bias |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | COMBINE ERMSD OPES_EXPANDED ECV_MULTITHERMAL PYTORCH_MODEL RESTART COORDINATION MOLINFO ENERGY OPES_METAD_EXPLORE VOLUME PRINT | setup function pytorch generic opes colvar |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | COMBINE METAD UPPER_WALLS DISTANCE CENTER MOLINFO RESTRAINT DUMPMASSCHARGE FIXEDATOM PRINT | function generic vatom colvar bias |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | MATHEVAL METAD UPPER_WALLS DISTANCE RESTART DUMPATOMS FIT_TO_TEMPLATE WRAPAROUND UNITS GROUP COM WHOLEMOLECULES PRINT FLUSH DISTANCES POSITION LOWER_WALLS | setup vatom function multicolvar core generic colvar bias |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | UPPER_WALLS DISTANCE COORDINATION COM GYRATION PBMETAD PRINT | vatom generic colvar bias |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | TORSION MOLINFO GROUP GYRATION PRINT PBMETAD WHOLEMOLECULES | core bias colvar generic |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | UPPER_WALLS METAD CUSTOM LOCAL_AVERAGE Q6 Q4 PIV FUNCPATHMSD PAIRENTROPY ENERGY RESTRAINT UNITS VOLUME PRINT | setup function symfunc piv gridtools generic colvar bias |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | METAD CUSTOM DISTANCE UNITS COM BIASVALUE DRR FLUSH PRINT | setup function generic vatom drr colvar bias |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | LOAD MOLINFO GROUP BIASVALUE WHOLEMOLECULES EMMIVOX PRINT | setup isdb core generic bias |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | TORSION BF_FOURIER TD_UNIFORM OPT_AVERAGED_SGD VES_LINEAR_EXPANSION PRINT | generic colvar ves |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | MATHEVAL UPPER_WALLS PYTORCH_MODEL DISTANCE COORDINATION COMMITTOR ANGLE LOAD CENTER FIT_TO_TEMPLATE ENERGY GROUP WHOLEMOLECULES FLUSH ENDPLUMED FIXEDATOM PRINT | setup vatom function pytorch core generic colvar 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 | TORSION METAD UPPER_WALLS CUSTOM DISTANCE UNITS COM LOWER_WALLS PRINT | setup function generic vatom colvar bias |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | UPPER_WALLS DISTANCE MOLINFO COM GYRATION PBMETAD PRINT | vatom generic 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 | METAD UPPER_WALLS COORDINATION DIHCOR MOLINFO ALPHARMSD PARABETARMSD GROUP ENERGY ANTIBETARMSD GYRATION WHOLEMOLECULES LOWER_WALLS RANDOM_EXCHANGES PRINT | secondarystructure multicolvar core generic colvar bias |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | TORSION CONTACTMAP METAD SAXS CENTER MOLINFO STATS ENSEMBLE ANTIBETARMSD GYRATION WHOLEMOLECULES ALPHABETA BIASVALUE PBMETAD PRINT | function isdb secondarystructure generic multicolvar vatom colvar bias |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | BF_CHEBYSHEV UPPER_WALLS HISTOGRAM REWEIGHT_METAD RESTRAINT COORDINATIONNUMBER CONVERT_TO_FES METAD COORDINATION UNITS DUMPGRID REWEIGHT_BIAS LOWER_WALLS COMBINE TD_GRID LOAD FLUSH ANGLES DISTANCE UWALLS EXTERNAL OPT_AVERAGED_SGD DISTANCES VES_LINEAR_EXPANSION PRINT | setup function ves symfunc multicolvar gridtools generic colvar bias |
| 21.004 | Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy | bio | machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding | Dorothea Gobbo | PATHMSD METAD UPPER_WALLS RESTART WHOLEMOLECULES LOWER_WALLS PRINT | setup generic colvar bias |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | COMBINE MATHEVAL METAD RMSD UPPER_WALLS DISTANCE CENTER MOLINFO ENERGY WHOLEMOLECULES LOWER_WALLS PRINT | function generic vatom colvar bias |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | TORSION MATHEVAL UPPER_WALLS PYTORCH_MODEL DISTANCE LOAD UNITS GROUP COM OPES_METAD FLUSH ENDPLUMED LOWER_WALLS PRINT | setup function pytorch generic core vatom opes colvar bias |
| 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 | UPPER_WALLS HISTOGRAM ENERGY CONVERT_TO_FES REWEIGHT_TEMP_PRESS MATHEVAL CELL RESTART READ TD_MULTITHERMAL_MULTIBARIC DUMPGRID REWEIGHT_BIAS COMBINE LOAD VOLUME BF_LEGENDRE Q6 OPT_DUMMY PRINT OPT_AVERAGED_SGD VES_LINEAR_EXPANSION TD_WELLTEMPERED LOWER_WALLS | setup function ves symfunc gridtools generic colvar bias |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | COMBINE TORSION CUSTOM DISTANCE ANGLE DUMPDERIVATIVES CENTER RESTRAINT GROUP ENDPLUMED PRINT | function generic core vatom colvar bias |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | TORSION ERMSD RMSD METAD DISTANCE MOLINFO WHOLEMOLECULES PRINT | generic colvar bias |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | RESTART MOVINGRESTRAINT COM INPLANEDISTANCES FLUSH DISTANCES PRINT | setup vatom multicolvar generic bias |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | FIND_CONTOUR_SURFACE FCCUBIC CENTER UNITS GROUP MULTICOLVARDENS FOURIER_TRANSFORM DUMPGRID MORE_THAN | setup function contour symfunc fourier core gridtools vatom |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | UPPER_WALLS METAD FCCUBIC CELL UNITS ENDPLUMED PRINT | setup symfunc generic colvar bias |
| 19.046 | Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding | bio | VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation | Faidon Brotzakis | TORSION COMBINE RMSD UPPER_WALLS DISTANCE METAD REWEIGHT_METAD MOLINFO COM FUNNEL GROUP WHOLEMOLECULES ALPHABETA LOWER_WALLS DISTANCES BRIDGE PRINT | function adjmat generic multicolvar core vatom funnel colvar bias |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | UPPER_WALLS METAD RMSD DISTANCE COM FUNNEL WHOLEMOLECULES LOWER_WALLS FUNNEL_PS PRINT | generic vatom funnel colvar bias |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | MATHEVAL METAD UPPER_WALLS COORDINATION HISTOGRAM REWEIGHT_METAD READ WRAPAROUND FIT_TO_TEMPLATE GROUP COM WHOLEMOLECULES DUMPGRID CONVERT_TO_FES FLUSH ENDPLUMED POSITION PRINT | vatom function gridtools core generic colvar bias |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | RMSD UPPER_WALLS DISTANCE SAXS CENTER MOLINFO STATS RESTRAINT GROUP BIASVALUE WHOLEMOLECULES ENDPLUMED INCLUDE PRINT | function isdb generic core vatom colvar 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 | RMSD LOWER_WALLS PRINT COMBINE MOLINFO FUNNEL_PS UNITS DISTANCE PATHMSD UPPER_WALLS COM WHOLEMOLECULES ANGLE ENDPLUMED FUNNEL METAD MATHEVAL | funnel bias generic function setup vatom colvar |
| 25.027 | Enhanced-sampling MD simulations of a protein-peptide complex integrating SAXS and XL-MS experimental information | bio | steered MD, metadynamics, SAXS, XL-MS, ensemble reconstruction | Mattia Bernetti | CENTER PRINT MOLINFO MOVINGRESTRAINT DISTANCE UPPER_WALLS WHOLEMOLECULES INCLUDE METAD GROUP SAXS GYRATION | bias generic vatom core colvar isdb |
| 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 RMSD PRINT COMBINE MOLINFO DISTANCE GHOST ENERGY CUSTOM OPES_METAD_EXPLORE GROUP COORDINATION ECV_MULTITHERMAL OPES_EXPANDED | opes generic function vatom core colvar |
| 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 MOLINFO PUCKERING MOVINGRESTRAINT DISTANCE TORSION METAD RESTART RESTRAINT | setup generic colvar bias |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | LOWER_WALLS FLUSH BIASVALUE MOLINFO COORDINATION MATHEVAL RMSD POSITION PRINT FIT_TO_TEMPLATE UNITS DISTANCE METAD CENTER COMBINE ENERGY OPES_METAD OPES_METAD_EXPLORE GROUP PYTORCH_MODEL CONTACTMAP FIXEDATOM UPPER_WALLS INCLUDE CUSTOM ENDPLUMED WHOLEMOLECULES | pytorch bias opes generic function setup vatom core colvar |
| 24.014 | Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation | methods | data augmentation, geodesic interpolation, collective variables, protein folding | Juno Nam | RMSD LOWER_WALLS FLUSH PRINT MOLINFO UPPER_WALLS WHOLEMOLECULES METAD PYTORCH_MODEL DRR COORDINATION | pytorch bias generic drr colvar |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | CENTER POSITION METAD FLUSH PRINT UNITS DISTANCE COM CUSTOM DISTANCES WHOLEMOLECULES GROUP | bias generic function setup vatom core colvar multicolvar |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | Q6 PRINT COMBINE Q4 ENERGY COORDINATIONNUMBER METAD VOLUME MATHEVAL | bias generic function colvar symfunc |
| 23.035 | An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors | bio | G protein coupled receptor, peptide ligands, metadynamics, multiple-walker | Timothy Clark | CENTER LOWER_WALLS BIASVALUE PRINT DISTANCE UPPER_WALLS WHOLEMOLECULES CONSTANT METAD MATHEVAL | bias generic function vatom colvar |
| 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 | ENSEMBLE CENTER RMSD BIASVALUE PRINT MOLINFO DISTANCE UPPER_WALLS GROUP WRAPAROUND SAXS STATS | bias generic function vatom core colvar isdb |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | FIXEDATOM LOWER_WALLS FLUSH PRINT UNITS DISTANCE ENERGY UPPER_WALLS COM OPES_METAD COMMITTOR COORDINATIONNUMBER DISTANCES ZDISTANCES CUSTOM GROUP MATHEVAL | bias opes generic function setup vatom core colvar symfunc multicolvar |
| 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 | CENTER FIXEDATOM LOWER_WALLS PRINT GROUP FIT_TO_TEMPLATE UNITS DISTANCE PATH UPPER_WALLS OPES_METAD CUSTOM OPES_METAD_EXPLORE TORSION WHOLEMOLECULES PYTORCH_MODEL COORDINATION | pytorch bias opes generic function setup mapping vatom core colvar |
| 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 | LOWER_WALLS FLUSH BIASVALUE PRINT UNITS PATHMSD UPPER_WALLS CUSTOM METAD DRR TIME | bias generic function setup drr colvar |
| 22.023 | Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy | bio | CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble | Faidon Brotzakis | RMSD PRINT BIASVALUE MOLINFO RESTART EMMI PBMETAD UPPER_WALLS COM TORSION WHOLEMOLECULES GROUP COORDINATION | bias generic setup vatom core colvar isdb |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | RMSD LOWER_WALLS FLUSH PRINT COMBINE FIT_TO_TEMPLATE BRIDGE UNITS DISTANCE UPPER_WALLS WHOLEMOLECULES ANGLE DISTANCES METAD GROUP COORDINATION MATHEVAL | bias generic function adjmat setup core colvar multicolvar |
| 22.005 | Collective Variable for Metadynamics Derived from AlphaFold Output | bio | AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable | Vojtech Spiwok | LOAD WHOLEMOLECULES PRINT METAD | setup generic bias |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | LOWER_WALLS PRINT GROUP UNITS DISTANCE UPPER_WALLS OPES_METAD COM LOAD CUSTOM OPES_METAD_EXPLORE PYTORCH_MODEL COORDINATION MATHEVAL | pytorch bias opes generic function setup vatom core colvar |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | PRINT BIASVALUE COMBINE MOLINFO ERMSD WHOLEMOLECULES METAD COORDINATION | function generic colvar bias |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | ENSEMBLE LOWER_WALLS PRINT COMBINE MOVINGRESTRAINT UNITS UPPER_WALLS LOAD CUSTOM TORSION CONSTANT METAD RESTRAINT | bias generic function setup colvar |
| 21.040 | A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms | bio | EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference | Faidon Brotzakis | BIASVALUE PRINT MOLINFO EMMI RESTART DISTANCE UPPER_WALLS COM WHOLEMOLECULES GROUP | bias generic setup vatom core colvar isdb |
| 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 PRINT DISTANCE UPPER_WALLS | generic colvar 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 | BIASVALUE PRINT UNITS DISTANCE ENERGY INCLUDE CUSTOM CONSTANT REWEIGHT_METAD METAD TORSION | bias generic function setup colvar |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | LOWER_WALLS PRINT FUNNEL_PS DISTANCE UPPER_WALLS COM FUNNEL METAD | funnel bias generic vatom colvar |
| 21.010 | Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry | chemistry | Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis | Théo Magrino | generic | |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | CENTER PRINT FIT_TO_TEMPLATE DISTANCE METAD RESTART | bias generic setup vatom colvar |
| 19.073 | On the role of enthalpic and entropic contributions on the conformational free energy landscape of MIL-101(Cr) building units | materials | metadynamics, MOF, MIL101Cr, conformational | Matteo Salvalaglio | LOWER_WALLS PRINT ENERGY UPPER_WALLS DISTANCES COORDINATIONNUMBER ENDPLUMED METAD GYRATION | bias generic colvar symfunc multicolvar |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | POSITION PRINT MAZE_OPTIMIZER_BIAS UNITS MAZE_SIMULATED_ANNEALING MAZE_LOSS | maze generic colvar setup |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | LOWER_WALLS FLUSH PRINT COMBINE UNITS DISTANCE UPPER_WALLS ENERGY METAD | bias generic function setup colvar |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | FLUSH PRINT UNITS DISTANCE UPPER_WALLS METAD RESTART MATHEVAL | bias generic function setup colvar |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | PRINT COMBINE RESTART ALPHABETA DISTANCE COM COMMITTOR TORSION WHOLEMOLECULES EXTERNAL | bias generic function setup vatom colvar multicolvar |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | LOWER_WALLS PRINT COMBINE ENERGY UPPER_WALLS CELL TORSION ENDPLUMED METAD VOLUME MATHEVAL | function generic colvar bias |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | BIASVALUE MOLINFO PUCKERING INCLUDE TORSION CONSTANT MATHEVAL | function generic colvar bias |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | PRINT BIASVALUE MOLINFO EMMI GROUP | isdb core generic bias |
| 25.024 | Sampling glycan-glycan interactions for B22 calculations | bio | B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange | Isabell Louise Grothaus | COMBINE METAD DISTANCE RESTRAINT POSITION COM PRINT | function vatom colvar generic bias |
| 25.022 | Imidazole Diffusion in SALEM-2 MOF | materials | OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials | Sudheesh Kumar Ethirajan | ENDPLUMED PROJECTION_ON_AXIS MOLINFO WHOLEMOLECULES DISTANCE DISTANCES GROUP UNITS CENTER OPES_METAD PRINT | vatom colvar multicolvar setup opes generic core |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | ABMD WHOLEMOLECULES DISTANCE COMMITTOR GROUP COM FLUSH PRINT | vatom colvar bias generic core |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | DUMPGRID REWEIGHT_METAD RESTART METAD COORDINATION DISTANCE CUSTOM GROUP READ HISTOGRAM UPPER_WALLS FLUSH PRINT | function colvar gridtools setup generic core bias |
| 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 | COMBINE ECV_MULTITHERMAL RESTART COORDINATION OPES_EXPANDED DISTANCE CUSTOM GROUP OPES_METAD_EXPLORE TORSION ENERGY PRINT | function colvar setup opes generic 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 | MOLINFO GROUP TORSION METAD COORDINATION WHOLEMOLECULES DISTANCE MATHEVAL UPPER_WALLS CENTER ANGLE COMBINE FIT_TO_TEMPLATE OPES_METAD ENDPLUMED CONTACTMAP CUSTOM COMMITTOR RMSD FIXEDATOM PRINT | function vatom colvar opes generic 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 |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | BIASVALUE INCLUDE MOLINFO WHOLEMOLECULES GROUP ERMSD RESTRAINT EMMIVOX PRINT | colvar isdb bias generic core |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | BIASVALUE DISTANCE CUSTOM UNITS PRINT | function colvar setup generic bias |
| 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 | COMBINE DISTANCE CUSTOM COMMITTOR LOWER_WALLS UNITS UPPER_WALLS TORSION FLUSH OPES_METAD PRINT | function colvar setup opes generic bias |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | BIASVALUE ENDPLUMED CUSTOM LOWER_WALLS PYTORCH_MODEL UNITS POSITION UPPER_WALLS OPES_METAD PRINT | function pytorch colvar setup opes generic bias |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | PATHMSD VSTACK VORONOI LANDMARK_SELECT_FPS DISSIMILARITIES SKETCHMAP METAD COLLECT_FRAMES WHOLEMOLECULES DISTANCE TRANSPOSE CUSTOM SKETCHMAP_PROJECTION UPPER_WALLS COM PRINT | function vatom colvar matrixtools landmarks generic valtools bias dimred |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | COMBINE Q6 LOCAL_Q6 CLUSTER_NATOMS LOCAL_Q4 DFSCLUSTERING COORDINATIONNUMBER MFILTER_LESS CONTACT_MATRIX Q4 GROUP MFILTER_MORE LOCAL_AVERAGE PRINT | function adjmat multicolvar generic clusters core symfunc |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | ENDPLUMED OPES_EXPANDED POSITION TORSION UNITS OPES_METAD ECV_MULTITHERMAL ENERGY PRINT | generic colvar setup opes |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | LOAD COMBINE Q6 INCLUDE METAD COORDINATIONNUMBER Q4 GROUP MATHEVAL PAIRENTROPY CENTER PRINT | function vatom gridtools setup generic core symfunc bias |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | DISTANCE DISTANCES METAD PRINT | generic colvar bias multicolvar |
| 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 METAD CUSTOM FLUSH PRINT | function colvar generic drr bias |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | GYRATION METAD COORDINATION WHOLEMOLECULES GROUP LOWER_WALLS UPPER_WALLS FLUSH PRINT | generic colvar core bias |
| 22.016 | Homogeneous ice nucleation in an ab initio machine learning model of water | chemistry | ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces | Pablo Piaggi | VOLUME DUMPGRID HISTOGRAM RESTART OPES_METAD AROUND CUSTOM ENVIRONMENTSIMILARITY UPPER_WALLS ENERGY PRINT | function colvar gridtools envsim opes setup generic volumes bias |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | LOAD COMBINE VOLUME TD_WELLTEMPERED BF_LEGENDRE RESTART METAD VES_LINEAR_EXPANSION OPT_AVERAGED_SGD PAIRENTROPY ENERGY PRINT | function colvar ves gridtools setup generic bias |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | DISTANCES GROUP LOWER_WALLS TORSION COORDINATION WHOLEMOLECULES DISTANCE PYTORCH_MODEL MATHEVAL UNITS CENTER UPPER_WALLS ANGLE LOAD FIT_TO_TEMPLATE OPES_METAD ENDPLUMED FIXEDATOM PRINT | pytorch function colvar vatom multicolvar setup opes generic core bias |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | LOAD DUMPGRID CLUSTER_NATOMS DFSCLUSTERING AROUND COORDINATIONNUMBER DENSITY CONTACT_MATRIX CLUSTER_DISTRIBUTION GROUP MFILTER_MORE RESTRAINT MULTICOLVARDENS FIXEDATOM PRINT | vatom gridtools adjmat multicolvar bias setup generic clusters core volumes symfunc |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | BIASVALUE RESTART PBMETAD WHOLEMOLECULES CONSTANT MATHEVAL TORSION PRINT | function colvar setup generic bias |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | DUMPGRID REWEIGHT_METAD INCLUDE METAD COORDINATION PUCKERING MOLINFO WHOLEMOLECULES DISTANCE GROUP LOWER_WALLS HISTOGRAM UPPER_WALLS RANDOM_EXCHANGES ENERGY PRINT | colvar gridtools generic core bias |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | WHOLEMOLECULES DISTANCE GROUP COM PRINT | vatom generic colvar core |
| 20.034 | Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations | bio | RNA, SARS-CoV-2, partial tempering | Sandro Bottaro | RESTART ABMD MOLINFO DISTANCE ERMSD CENTER TORSION PRINT | vatom colvar setup generic bias |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | PBMETAD COORDINATION WHOLEMOLECULES CENTER PRINT | vatom generic colvar bias |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | DUMPGRID REWEIGHT_METAD METAD CONVERT_TO_FES MULTI_RMSD RESTRAINT HISTOGRAM PRINT | generic colvar gridtools bias |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | LOWER_WALLS FLUSH REWEIGHT_METAD METAD COORDINATION CONTACT_MATRIX DISTANCE PAIRENTROPY UNITS HISTOGRAM CENTER UPPER_WALLS ENERGY LOAD COMBINE DUMPGRID SPRINT VOLUME Q6 COORDINATIONNUMBER DENSITY LOCAL_AVERAGE REWEIGHT_BIAS CONVERT_TO_FES PRINT | vatom function colvar gridtools adjmat setup sprint generic volumes symfunc bias |
| 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 DUMPGRID READ REWEIGHT_METAD ENDPLUMED METAD ABMD DISTANCE CONVERT_TO_FES MATHEVAL LOWER_WALLS HISTOGRAM UPPER_WALLS COM PRINT | function vatom colvar gridtools generic bias |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | MOVINGRESTRAINT GYRATION ENDPLUMED UNITS PRINT | generic colvar setup bias |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | PATHMSD RESTART METAD LOWER_WALLS UNITS UPPER_WALLS PRINT | generic colvar setup bias |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | GYRATION METAD MOLINFO DISTANCE UPPER_WALLS COM ENERGY PRINT | vatom generic colvar bias |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | PATHMSD METAD WHOLEMOLECULES LOWER_WALLS UPPER_WALLS PRINT | generic colvar bias |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | COMBINE ENSEMBLE BIASVALUE SAXS ENDPLUMED INCLUDE COORDINATION PBMETAD MOLINFO WHOLEMOLECULES STATS GROUP MATHEVAL CENTER ANGLE ALPHABETA PRINT | function vatom colvar multicolvar isdb generic core bias |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | FUNCPATHMSD ENDPLUMED METAD CONTACTMAP WHOLEMOLECULES DISTANCE RMSD COM PRINT | function vatom colvar generic 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 | GYRATION ENSEMBLE BIASVALUE JCOUPLING ENDPLUMED PBMETAD MOLINFO WHOLEMOLECULES CS2BACKBONE STATS RDC METAINFERENCE TORSION FLUSH PRINT | function colvar isdb generic bias |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | DRR TORSION PRINT | generic colvar drr |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | ENDPLUMED METAD MOLINFO WHOLEMOLECULES RMSD ERMSD PRINT | generic colvar bias |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | LOAD PRINT ENDPLUMED RESTART METAD UNITS POSITION TORSION ENERGY VES_DELTA_F | colvar ves setup generic bias |