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 | WHOLEMOLECULES MOLINFO CONTACTMAP PRINT COM DISTANCE GROUP PBMETAD GYRATION ALPHARMSD INCLUDE DUMPMASSCHARGE COORDINATION | vatom bias secondarystructure colvar core generic |
| 25.030 | Committor Regularization | methods | metadynamics, enhanced sampling, mlcvs, committor, machine learning | Florian Dietrich | METAD MOVINGRESTRAINT PRINT UNITS | bias setup generic |
| 25.024 | Sampling glycan-glycan interactions for B22 calculations | bio | B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange | Isabell Louise Grothaus | RESTRAINT METAD PRINT COM DISTANCE POSITION COMBINE | function vatom bias colvar generic |
| 25.023 | Molecular simulations of Tau-protein oligomers | bio | metadynamics, proteins, aggregation | Giovanni Bussi | HISTOGRAM RESTRAINT RMSD CONVERT_TO_FES CONTACTMAP METAD PRINT CUSTOM REWEIGHT_BIAS FLUSH DUMPGRID RESTART | function setup bias colvar gridtools generic |
| 25.012 | A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis | bio | enzyme catalysis, transition state, structure-activity relationship, free energy surface, reaction mechanism, water, alpha-amylase, sugar, QM/MM MD, OPES, committor function, machine learning | Sudip Das | OPES_METAD MATHEVAL COORDINATION BIASVALUE PRINT TORSION CELL CUSTOM LOAD FLUSH DISTANCE UNITS ENERGY INCLUDE POSITION COMBINE | function setup opes bias colvar generic |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | OPES_METAD WHOLEMOLECULES MOLINFO MATHEVAL PRINT TORSION CUSTOM PYTORCH_MODEL DISTANCE GROUP ENDPLUMED ENERGY COMMITTOR COMBINE | function opes pytorch colvar core 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 | WHOLEMOLECULES MOLINFO DIHCOR ANTIBETARMSD TORSION PRINT PARABETARMSD COMBINE FLUSH DISTANCE GROUP PBMETAD GYRATION ALPHARMSD ENDPLUMED INCLUDE COORDINATION | function multicolvar secondarystructure bias colvar core generic |
| 24.024 | Host-Guest binding free energies à la carte, an automated OneOPES protocol | bio | OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest | Valerio Rizzi | WHOLEMOLECULES MATHEVAL FIT_TO_TEMPLATE ENERGY ECV_MULTITHERMAL PRINT TORSION CENTER OPES_METAD_EXPLORE ANGLE DISTANCE GROUP ENDPLUMED UPPER_WALLS FIXEDATOM OPES_EXPANDED LOWER_WALLS COORDINATION | function vatom opes bias colvar core generic |
| 24.022 | Integrating Path Sampling with Enhanced Sampling for Rare-event Kinetics | methods | OPES Flooding, Weighted Ensemble, Metadynamics, Kinetics, Infrequent Metadynamics, Integrated Sampling | Dhiman Ray | MATHEVAL CONTACTMAP CENTER GROUP ENDPLUMED UPPER_WALLS TORSION ANGLE DISTANCE FIXEDATOM COMBINE WHOLEMOLECULES OPES_METAD FIT_TO_TEMPLATE MOLINFO RMSD METAD PRINT CUSTOM COMMITTOR COORDINATION | function vatom opes bias colvar core generic |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | METAD TORSION PRINT GROUP UNITS | setup bias colvar core generic |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | BIASVALUE PRINT CUSTOM DISTANCE UNITS | function setup bias colvar generic |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | METAD PRINT LOAD GROUP INCLUDE RESTART | bias core setup generic |
| 23.045 | Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state | bio | Path CVs Metadynamics, GPCRs activation transition | Vittorio Limongelli | PATHMSD MOLINFO CONTACTMAP METAD PRINT DISTANCE FUNCPATHMSD UPPER_WALLS ALPHARMSD INCLUDE LOWER_WALLS | function bias secondarystructure colvar generic |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | HISTOGRAM CONVERT_TO_FES METAD PRINT READ GROUP ENDPLUMED DUMPGRID COMMITTOR COORDINATION | bias colvar gridtools core generic |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | RESTRAINT MOLINFO METAD PRINT CENTER DISTANCE UPPER_WALLS FIXEDATOM DUMPMASSCHARGE COMBINE | function vatom bias colvar generic |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | PRINT COM GYRATION DISTANCE PBMETAD UPPER_WALLS COORDINATION | bias colvar generic vatom |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | WHOLEMOLECULES METAD TORSION COM PRINT DISTANCE FLUSH UPPER_WALLS COMBINE | function vatom bias colvar generic |
| 23.013 | Path meta-eABF simulation of large scale conformational change in STING protein | methods | meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint | Istvan Kolossvary | PATHMSD DRR TIME METAD BIASVALUE PRINT CUSTOM FLUSH UNITS UPPER_WALLS LOWER_WALLS | function setup bias colvar drr 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 | MATHEVAL DRMSD METAD PRINT CELL CUSTOM UPPER_WALLS COMMITTOR LOWER_WALLS | bias colvar function generic |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | WHOLEMOLECULES TORSION PRINT | colvar generic |
| 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 | colvar generic |
| 22.011 | Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck | methods | metadynamics, membrane permeation, protein folding | Shams Mehdi | WHOLEMOLECULES MOLINFO MATHEVAL METAD PRINT COM CUSTOM YANGLES TORSION DISTANCE ZANGLES XANGLES UPPER_WALLS ALPHABETA LOWER_WALLS COMBINE | function vatom multicolvar bias colvar generic |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | DISTANCE PRINT CENTER | colvar generic vatom |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | HISTOGRAM CLUSTER_NATOMS DFSCLUSTERING METAD Q6 PRINT COORDINATIONNUMBER CONTACT_MATRIX CLUSTER_DISTRIBUTION MFILTER_MORE LOCAL_Q6 GROUP DUMPGRID FIXEDATOM INSPHERE COMBINE | symfunc clusters volumes function vatom multicolvar adjmat bias gridtools core generic |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | MOLINFO ENERGY PRINT COM GYRATION DISTANCE PBMETAD UPPER_WALLS LOWER_WALLS | bias colvar generic vatom |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | WHOLEMOLECULES MOLINFO CONTACTMAP METAD PRINT REWEIGHT_BIAS GROUP PBMETAD ALPHARMSD ALPHABETA RESTART | setup multicolvar bias secondarystructure colvar core 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 ECV_UMBRELLAS_LINE PRINT TORSION ENDPLUMED ENERGY OPES_EXPANDED | generic colvar opes |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | TORSION PRINT ENDPLUMED | colvar 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 | RESTRAINT WHOLEMOLECULES MOLINFO STATS PRINT COORDINATION | bias colvar function generic |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | WHOLEMOLECULES MOLINFO METAINFERENCE STATS ENSEMBLE TORSION PRINT CENTER SAXS DISTANCE FLUSH PBMETAD GYRATION ALPHABETA | isdb function vatom multicolvar bias colvar generic |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | METAD PRINT COORDINATIONNUMBER COMBINE FLUSH ENDPLUMED GROUP DISTANCES UPPER_WALLS UNITS RESTART | symfunc function setup multicolvar bias core generic |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | HISTOGRAM OPT_AVERAGED_SGD TD_GRID VES_LINEAR_EXPANSION CONVERT_TO_FES EXTERNAL PRINT COMBINE ANGLE DISTANCE FLUSH TD_WELLTEMPERED UNITS UPPER_WALLS BF_CHEBYSHEV DUMPGRID LOWER_WALLS COORDINATION | function setup ves bias colvar gridtools generic |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | MOLINFO UPPER_WALLS METAD PRINT COM GYRATION DISTANCE ENERGY | bias colvar generic vatom |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | HISTOGRAM CONVERT_TO_FES METAD PRINT COMBINE REWEIGHT_BIAS READ UPPER_WALLS DUMPGRID DISTANCE_FROM_CONTOUR RESTART | function setup bias gridtools contour generic |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | OUTER_PRODUCT MORE_THAN DFSCLUSTERING METAD PRINT COORDINATIONNUMBER CUSTOM ONES CLUSTER_DISTRIBUTION CLUSTER_PROPERTIES SMAC LOCAL_Q6 DISTANCES OUTPUT_CLUSTER CLUSTER_NATOMS CONTACT_MATRIX MATRIX_VECTOR_PRODUCT Q6 | symfunc clusters function multicolvar adjmat matrixtools bias generic |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | WHOLEMOLECULES MATHEVAL METAD BIASVALUE PRINT COM DISTANCE UPPER_WALLS CONSTANT LOWER_WALLS | function vatom bias colvar generic |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | RDC WHOLEMOLECULES MOLINFO CS2BACKBONE METAINFERENCE STATS ENSEMBLE BIASVALUE TORSION PRINT GYRATION JCOUPLING FLUSH ENDPLUMED PBMETAD | isdb function bias colvar generic |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | WHOLEMOLECULES METAD TORSION PRINT GYRATION | bias colvar generic |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | RESTRAINT WHOLEMOLECULES MOLINFO RMSD STATS BIASVALUE PRINT CENTER SAXS DISTANCE GROUP ENDPLUMED UPPER_WALLS INCLUDE | isdb function vatom bias colvar core generic |
| 26.008 | Ensemble Dynamics | methods | State Exploration, Protein Folding, Drug Binding, Phase Transition | Florian M. Dietrich | OPES_METAD_EXPLORE LOAD TORSION BIASVALUE DISTANCE CELL CUSTOM GROUP PRINT POSITION UNITS | generic bias function core opes colvar setup |
| 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 OPES_METAD_EXPLORE COORDINATION PATH OPES_EXPANDED PATHMSD DISTANCE ENERGY LOWER_WALLS RMSD CUSTOM CENTER GROUP PRINT VOLUME ECV_MULTITHERMAL | bias function core mapping opes colvar vatom generic |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | FLUSH COMMITTOR DISTANCE ABMD COM GROUP PRINT WHOLEMOLECULES | bias core colvar vatom generic |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | POSITION RESTRAINT PRINT UNITS | generic colvar bias setup |
| 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 | COMBINE OPES_METAD COORDINATION TORSION DISTANCE CUSTOM MOLINFO PRINT GYRATION ALPHARMSD WHOLEMOLECULES | function opes secondarystructure colvar generic |
| 24.014 | Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation | methods | data augmentation, geodesic interpolation, collective variables, protein folding | Juno Nam | METAD UPPER_WALLS FLUSH COORDINATION LOWER_WALLS RMSD DRR MOLINFO PRINT PYTORCH_MODEL WHOLEMOLECULES | bias drr pytorch colvar generic |
| 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 INCLUDE COORDINATION TORSION DISTANCE ALPHABETA COM PRINT GYRATION WHOLEMOLECULES | bias multicolvar colvar vatom generic |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | METAD INCLUDE LOAD COORDINATIONNUMBER CENTER GROUP PRINT | bias symfunc core setup vatom generic |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | UPPER_WALLS OPES_METAD ENDPLUMED BIASVALUE LOWER_WALLS CUSTOM PRINT PYTORCH_MODEL POSITION UNITS | bias function setup opes pytorch colvar generic |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | METAD UPPER_WALLS VSTACK LANDMARK_SELECT_FPS SKETCHMAP PATHMSD DISTANCE DISSIMILARITIES TRANSPOSE COLLECT_FRAMES COM CUSTOM VORONOI PRINT SKETCHMAP_PROJECTION WHOLEMOLECULES | dimred bias function matrixtools valtools landmarks colvar vatom generic |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | METAD MATHEVAL DISTANCE REWEIGHT_METAD READ RMSD CONVERT_TO_FES MOLINFO PRINT DUMPGRID HISTOGRAM WHOLEMOLECULES | bias function gridtools colvar generic |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | CONTACTMAP ECV_UMBRELLAS_LINE OPES_EXPANDED ECV_MULTITHERMAL ENERGY PRINT WHOLEMOLECULES | opes colvar generic |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | UPPER_WALLS MATHEVAL METAD COMBINE FLUSH FIT_TO_TEMPLATE COORDINATION BRIDGE WHOLEMOLECULES DISTANCE LOWER_WALLS RMSD GROUP PRINT ANGLE UNITS DISTANCES | adjmat bias function core setup multicolvar colvar generic |
| 22.005 | Collective Variable for Metadynamics Derived from AlphaFold Output | bio | AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable | Vojtech Spiwok | METAD PRINT LOAD WHOLEMOLECULES | generic bias setup |
| 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 METAD ENDPLUMED ALPHABETA LOWER_WALLS GROUP PRINT GYRATION WHOLEMOLECULES | bias core multicolvar colvar generic |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | PRINT RMSD DISTANCE | colvar generic |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | LOAD DISTANCE RESTRAINT GROUP PRINT FIXEDATOM | generic bias core colvar vatom setup |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | UPPER_WALLS METAD COMBINE INCLUDE MOVINGRESTRAINT CONSTANT RESTRAINT PRINT | generic function bias |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | MATHEVAL TORSIONS DISTANCE COM KDE PRINT | function gridtools multicolvar colvar vatom generic |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | METAD PBMETAD CONTACTMAP ENSEMBLE TORSION STATS SAXS BIASVALUE ALPHABETA ANTIBETARMSD CENTER MOLINFO PRINT GYRATION WHOLEMOLECULES | bias function isdb multicolvar secondarystructure colvar vatom generic |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | MATHEVAL PBMETAD RESTART TORSION BIASVALUE CONSTANT PRINT WHOLEMOLECULES | bias function setup colvar generic |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | EMMI PRINT BIASVALUE READ DISTANCES RMSD GROUP MOLINFO CONVERT_TO_FES DUMPGRID HISTOGRAM WHOLEMOLECULES | bias core gridtools isdb multicolvar colvar generic |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | PBMETAD COORDINATION CENTER PRINT WHOLEMOLECULES | generic colvar vatom bias |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | METAD RESTART FIT_TO_TEMPLATE DISTANCE CENTER PRINT | bias setup colvar vatom generic |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | UPPER_WALLS MATHEVAL METAD CELL LOWER_WALLS ENERGY VOLUME PRINT | generic function bias colvar |
| 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 | UPPER_WALLS MATHEVAL RESTART TD_WELLTEMPERED OPT_AVERAGED_SGD OPT_DUMMY ENVIRONMENTSIMILARITY Q6 VOLUME PRINT VES_LINEAR_EXPANSION BF_LEGENDRE | generic envsim bias symfunc function ves 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 | METAD COORDINATION CUSTOM PRINT UNITS DISTANCES | bias function setup multicolvar colvar generic |
| 20.005 | Muscarinic M2 receptor/ligand Frequency-Adaptive Metadynamics and QM/MM calculations | bio | Frequency-adaptive metadynamics, multiple-walkers metadynamics, well-tempered metadynamics, GPCR, receptor, Adiabatic Bias MD | Riccardo Capelli | FLUSH PRINT DUMPGRID UPPER_WALLS FUNCPATHMSD COMBINE DISTANCE ABMD COM REWEIGHT_METAD READ MOLINFO HISTOGRAM CONTACTMAP METAD ENDPLUMED LOWER_WALLS CONVERT_TO_FES WHOLEMOLECULES | bias function gridtools colvar vatom 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 | UPPER_WALLS PBMETAD CS2BACKBONE FLUSH ENDPLUMED BIASVALUE ALPHABETA ANTIBETARMSD LOWER_WALLS GROUP MOLINFO PRINT WHOLEMOLECULES | bias core isdb secondarystructure multicolvar generic |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | METAD MATHEVAL SORT INCLUDE COORDINATION TORSION FLUSH DISTANCE COM MOLINFO PRINT MAXENT WHOLEMOLECULES | bias function colvar vatom generic |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | FLUSH MOVINGRESTRAINT INPLANEDISTANCES RESTART COM PRINT DISTANCES | bias setup multicolvar vatom generic |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | METAD UPPER_WALLS ENDPLUMED CELL LOWER_WALLS PRINT AROUND FCCUBIC UNITS | bias symfunc setup colvar generic volumes |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | METAD UPPER_WALLS MATHEVAL COMBINE TORSION ENDPLUMED CELL ENERGY LOWER_WALLS VOLUME PRINT | generic function bias colvar |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | METAD VES_DELTA_F RESTART TORSION LOAD ENDPLUMED ENERGY PRINT POSITION UNITS | bias ves setup colvar generic |
| 26.016 | Cryo-EM ensemble of the PilQ secretin | bio | EMMIVox, cryo-EM, ensemble | Tatiana I. Morozova | EMMIVOX GROUP PRINT MOLINFO WHOLEMOLECULES BIASVALUE | bias isdb generic core |
| 26.012 | Buprenorphine Restricts the Conformational Landscape of the μ-Opioid Receptor | bio | OneOPES, GPCR, MOR, activation, euclidean path, conformational changes, allostery | Simone Aureli | ENERGY DISTANCE VOLUME RMSD GROUP CENTER CUSTOM PRINT PATH ECV_MULTITHERMAL OPES_EXPANDED UPPER_WALLS COORDINATION OPES_METAD_EXPLORE | generic mapping bias core colvar opes vatom function |
| 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 | LOWER_WALLS DISTANCE GROUP MATHEVAL CENTER PRINT METAD GYRATION WHOLEMOLECULES UPPER_WALLS COORDINATION COMBINE | bias generic core colvar vatom function |
| 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 | MATHEVAL METAD OPES_METAD LOWER_WALLS GROUP COORDINATION WRAPAROUND CENTER COMMITTOR TORSION UPPER_WALLS COM DISTANCE FUNNEL_PS FUNNEL RMSD ENDPLUMED PRINT CUSTOM WHOLEMOLECULES | bias generic core vatom funnel colvar opes function |
| 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 | ENERGY DISTANCE GROUP MATHEVAL CENTER PRINT ANGLE WHOLEMOLECULES FIT_TO_TEMPLATE FIXEDATOM UPPER_WALLS COORDINATION OPES_METAD_EXPLORE | generic bias core colvar opes vatom function |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | RESTART DISTANCE GROUP COORDINATION FLUSH READ REWEIGHT_METAD CUSTOM METAD PRINT UPPER_WALLS DUMPGRID HISTOGRAM | gridtools setup bias generic core colvar function |
| 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 | DISTANCE GROUP COORDINATION CONVERT_TO_FES PRINT TORSION ANGLE WHOLEMOLECULES DUMPGRID HISTOGRAM | gridtools colvar generic core |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | RESTART MATHEVAL METAD ECV_MULTITHERMAL LOWER_WALLS GROUP CONTACTMAP COORDINATION OPES_METAD_EXPLORE WRAPAROUND MOLINFO TORSION UPPER_WALLS COM ENERGY CONSTANT RMSD INCLUDE PRINT CUSTOM OPES_EXPANDED WHOLEMOLECULES BIASVALUE PROJECTION_ON_AXIS | setup bias generic core vatom colvar opes function |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | COM LOWER_WALLS DISTANCE GHBFIX GROUP CENTER DEBUG PRINT METAD MOLINFO BIASVALUE UPPER_WALLS COORDINATION COMBINE | bias generic core colvar vatom function |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | CLUSTER_NATOMS DFSCLUSTERING UNITS PRINT METAD CLUSTER_PROPERTIES COORDINATIONNUMBER UPPER_WALLS CONTACT_MATRIX | setup bias generic symfunc clusters adjmat |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | RESTART UNITS PRINT METAD TORSION | bias colvar setup generic |
| 24.001 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | bio | OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis | Dhiman Ray | LOWER_WALLS DISTANCE UNITS COMMITTOR FLUSH CUSTOM PRINT TORSION OPES_METAD UPPER_WALLS COMBINE | setup bias generic colvar opes function |
| 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 | TRANSPOSE INCLUDE MATHEVAL SELECT_COMPONENTS FLUSH PRINT METAD SUM | valtools bias matrixtools generic function |
| 23.041 | Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference | methods | EMMIVox, cryo-EM, single-structure refinement, ensemble refinement, Bayesian inference, B-factors, structural ensembles | Samuel Hoff | EMMIVOX DISTANCE WRAPAROUND GROUP INCLUDE PRINT MOLINFO WHOLEMOLECULES BIASVALUE UPPER_WALLS | bias generic core colvar isdb |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | DISTANCE CONSTANT PBMETAD MATHEVAL PRINT ANGLE WHOLEMOLECULES BIASVALUE | bias colvar generic function |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | COM INCLUDE PBMETAD PRINT TORSION WHOLEMOLECULES GYRATION RESTRAINT COORDINATION | bias colvar vatom generic |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | COM DISTANCE ALPHARMSD CONTACTMAP PRINT METAD MOLINFO ANGLE DUMPFORCES | bias generic colvar vatom secondarystructure |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | PUCKERING CONVERT_TO_FES READ PRINT METAD MOLINFO TORSION DUMPGRID HISTOGRAM | gridtools colvar generic bias |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | COM LOWER_WALLS FUNNEL_PS DISTANCE FUNNEL PRINT METAD WHOLEMOLECULES PATHMSD UPPER_WALLS | bias generic funnel colvar vatom |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | DISTANCE CENTER COMMITTOR ENDPLUMED PRINT METAD TORSION COORDINATIONNUMBER | bias generic symfunc colvar vatom |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | COM DISTANCE UNITS PRINT METAD WHOLEMOLECULES PATHMSD UPPER_WALLS | setup bias generic colvar vatom |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | MATHEVAL REWEIGHT_METAD METAD DUMPGRID HISTOGRAM GROUP READ COORDINATION CONVERT_TO_FES UPPER_WALLS COM DISTANCE RMSD FLUSH ENDPLUMED PRINT WHOLEMOLECULES FIXEDATOM POSITION | gridtools generic bias core colvar vatom function |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | LOWER_WALLS DISTANCE ENERGY GROUP INCLUDE PUCKERING COORDINATION REWEIGHT_METAD PRINT METAD MOLINFO WHOLEMOLECULES UPPER_WALLS RANDOM_EXCHANGES DUMPGRID HISTOGRAM | gridtools generic bias core colvar |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | RESTRAINT DISTANCE ENSEMBLE INCLUDE GROUP CENTER STATS PRINT MOLINFO WHOLEMOLECULES BIASVALUE SAXS | generic bias core colvar isdb vatom function |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | PRINT METAD TORSION | bias colvar generic |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | DIHCOR INCLUDE PBMETAD PRINT MOLINFO GYRATION WHOLEMOLECULES COORDINATION ALPHABETA | bias colvar generic multicolvar |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | DISTANCE ENERGY GROUP UNITS MATHEVAL PRINT GYRATION FISST BIASVALUE RESTRAINT | setup generic bias core colvar fisst function |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | RESTART DISTANCE RMSD PRINT METAD MOLINFO TORSION WHOLEMOLECULES UPPER_WALLS COMBINE | setup bias generic colvar function |
| 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 GROUP PRINT METAD MOLINFO WHOLEMOLECULES PATHMSD UPPER_WALLS | setup bias generic core colvar |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | DISTANCE MATHEVAL COMMITTOR READ CONVERT_TO_FES PRINT METAD REWEIGHT_METAD REWEIGHT_BIAS TORSION EXTERNAL BIASVALUE DUMPGRID HISTOGRAM | gridtools generic bias colvar function |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | COM RESTART DISTANCE COMMITTOR PRINT TORSION WHOLEMOLECULES EXTERNAL COMBINE ALPHABETA | setup bias generic multicolvar colvar vatom function |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | RDC DISTANCE DIHCOR ENSEMBLE GROUP PBMETAD CENTER STATS PRINT ENDPLUMED MOLINFO TORSION WHOLEMOLECULES DHENERGY METAINFERENCE UPPER_WALLS RESTRAINT ALPHABETA | bias multicolvar generic core colvar isdb vatom function |
| 26.015 | Ensemble Dynamics | methods | State Exploration, Protein Folding, Drug Binding, Phase Transition | Florian M. Dietrich | CELL TORSION LOAD OPES_METAD_EXPLORE POSITION PRINT UNITS GROUP CUSTOM BIASVALUE DISTANCE | colvar opes bias generic setup function core |
| 26.010 | Solvation-Mediated Ammonia Synthesis in a Nanoheterogeneous Liquid Alloy | materials | OPES, Catalysis, Ammonia Synthesis | Axel Tosello Gardini | OPES_METAD_EXPLORE UPPER_WALLS INCLUDE PRINT COORDINATIONNUMBER DISTANCES OPES_METAD COORDINATION UNITS CUSTOM GROUP DISTANCE FLUSH | setup multicolvar colvar opes bias generic symfunc function core |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | MOLINFO TORSION POSITION WHOLEMOLECULES ENDPLUMED LOWER_WALLS PRINT METAD UPPER_WALLS CUSTOM ENERGY OPES_METAD UNITS GROUP RMSD BIASVALUE DISTANCE PYTORCH_MODEL | colvar opes bias generic setup pytorch function core |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | RESTART MOLINFO WHOLEMOLECULES UPPER_WALLS PRINT METAD COM GROUP FUNCPATHGENERAL DISTANCE | colvar bias generic setup vatom function core |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | TORSION LOAD PRINT CUSTOM COORDINATION ENERGY OPES_METAD GROUP DISTANCE COMBINE | colvar opes generic setup function core |
| 24.023 | Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21. A Machine-Learning-Aided Enhanced Sampling Study | bio | RNA, miRNA, OneOPES, ligand binding, conformational changes | Valerio Rizzi | RESTART TORSION OPES_METAD_EXPLORE PRINT CUSTOM COORDINATION ENERGY OPES_EXPANDED GROUP DISTANCE COMBINE ECV_MULTITHERMAL | colvar opes generic setup function core |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | MOLINFO UPPER_WALLS INCLUDE PRINT ENERGY OPES_EXPANDED WHOLEMOLECULES ECV_MULTITHERMAL CONTACTMAP | bias generic colvar opes |
| 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 | MATHEVAL MOLINFO WHOLEMOLECULES PRINT METAD RMSD DISTANCE | bias generic function colvar |
| 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 | MOLINFO SHADOW WRAPAROUND POSITION UPPER_WALLS PRINT DISTANCES METAD CENTER FIT_TO_TEMPLATE GROUP WHOLEMOLECULES | multicolvar colvar bias isdb generic vatom core |
| 23.029 | An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations | bio | SAXS, SANS, SAS, metainference, proteins, nucleic-acid | Federico Ballabio | MOLINFO SAXS WRAPAROUND UPPER_WALLS PRINT CENTER ENSEMBLE GROUP RMSD BIASVALUE DISTANCE STATS | colvar bias isdb generic vatom function core |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | MATHEVAL RESTART WRAPAROUND POSITION WHOLEMOLECULES LOWER_WALLS DISTANCES UPPER_WALLS METAD PRINT FIT_TO_TEMPLATE COM GROUP UNITS DISTANCE DUMPATOMS FLUSH | multicolvar colvar bias generic setup vatom function core |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | MOLINFO TORSION OPES_METAD_EXPLORE ENDPLUMED PRINT METAD ENERGY OPES_EXPANDED DISTANCE ECV_MULTITHERMAL | bias generic colvar opes |
| 23.004 | Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point | chemistry | water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential | Pablo Piaggi | ECV_UMBRELLAS_LINE RESTART DUMPGRID UPPER_WALLS PRINT ENVIRONMENTSIMILARITY LOWER_WALLS OPES_EXPANDED HISTOGRAM | gridtools opes bias envsim generic setup |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | TORSION CONSTANT INCLUDE OPES_METAD UNITS RMSD BIASVALUE CUSTOM PYTORCH_MODEL CONTACTMAP MOLINFO ENDPLUMED PRINT GROUP COMMITTOR COMBINE POSITION ENERGY WHOLEMOLECULES DISTANCE | colvar opes bias generic setup pytorch function core |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | TORSION TD_UNIFORM BF_FOURIER PRINT OPT_AVERAGED_SGD VES_LINEAR_EXPANSION | generic ves colvar |
| 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 | PRINT CENTER CONTACTMAP DISTANCE | generic vatom colvar |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | MATHEVAL GROUP OPES_METAD_EXPLORE LOAD UPPER_WALLS PRINT LOWER_WALLS COORDINATION OPES_METAD UNITS COM CUSTOM DISTANCE PYTORCH_MODEL | colvar opes bias pytorch generic setup vatom function core |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | MOLINFO ERMSD PRINT METAD COORDINATION WHOLEMOLECULES BIASVALUE COMBINE | bias generic function colvar |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | ANN LOAD TD_WELLTEMPERED CONSTANT OPT_AVERAGED_SGD MOVINGRESTRAINT OPES_METAD UPPER_WALLS UNITS CUSTOM BIASVALUE CONVERT_TO_FES DUMPGRID REWEIGHT_BIAS PRINT METAD COORDINATIONNUMBER REWEIGHT_METAD BF_CHEBYSHEV COMBINE HISTOGRAM FLUSH VES_LINEAR_EXPANSION RESTRAINT DISTANCE | gridtools colvar annfunc bias opes symfunc generic setup ves function |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | PAIRENTROPY LOAD Q6 DENSITY UPPER_WALLS LOCAL_AVERAGE CENTER COORDINATION UNITS CONVERT_TO_FES DUMPGRID REWEIGHT_BIAS LOWER_WALLS PRINT METAD COORDINATIONNUMBER SPRINT REWEIGHT_METAD COMBINE CONTACT_MATRIX HISTOGRAM FLUSH VOLUME ENERGY DISTANCE | vatom volumes sprint gridtools colvar adjmat bias generic setup symfunc function |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | MOLINFO LOAD PRINT EMMIVOX GROUP WHOLEMOLECULES BIASVALUE DUMPATOMS | bias isdb generic setup core |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | MATHEVAL FLUSH TORSION LOAD ENDPLUMED UPPER_WALLS PRINT LOWER_WALLS OPES_METAD UNITS COM GROUP DISTANCE PYTORCH_MODEL | colvar opes bias pytorch generic setup vatom function core |
| 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 | ENDPLUMED UPPER_WALLS DISTANCES LOWER_WALLS COORDINATIONNUMBER METAD ENERGY PRINT GYRATION | multicolvar colvar bias generic symfunc |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | EXTERNAL TORSION POSITION ENDPLUMED PRINT METAD OPES_METAD UNITS | colvar opes bias generic setup |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | RESTART LOWER_WALLS PRINT METAD UPPER_WALLS UNITS PATHMSD | bias generic setup colvar |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | MOLINFO UPPER_WALLS PRINT METAD ENERGY COM DISTANCE GYRATION | bias generic vatom colvar |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | UPPER_WALLS PRINT METAD LOWER_WALLS WHOLEMOLECULES PATHMSD | bias generic colvar |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | RESTART UPPER_WALLS LOWER_WALLS METAD CENTER PRINT COM GROUP DISTANCE | colvar bias generic setup vatom core |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | PBMETAD MATHEVAL MOLINFO COMBINE SAXS WHOLEMOLECULES ENDPLUMED INCLUDE PRINT CENTER COORDINATION ENSEMBLE ALPHABETA ANGLE GROUP BIASVALUE STATS | multicolvar colvar bias isdb generic vatom function core |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | MATHEVAL TORSION ENDPLUMED PRINT METAD | bias generic function colvar |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | PBMETAD RESTART MOLINFO ANTIBETARMSD WHOLEMOLECULES ENDPLUMED LOWER_WALLS UPPER_WALLS PRINT ALPHABETA GROUP CS2BACKBONE BIASVALUE FLUSH | multicolvar bias isdb secondarystructure generic setup core |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | RESTRAINT TORSION PRINT COM GROUP DISTANCE | colvar bias generic vatom core |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | RESTART PATH UPPER_WALLS DISTANCES METAD PRINT FLUSH | multicolvar bias mapping generic setup |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | EXTERNAL METAD COORDINATION ENERGY GROUP | bias colvar core |
| 26.009 | Exploring the Conformational Landscape of HIV-1 TAR RNA by PT-WTE | bio | RNA, PT-WTE, HIV-1 TAR | Stefano Bosio | ENERGY METAD WHOLEMOLECULES MOLINFO PRINT GROUP | colvar bias generic core |
| 26.004 | Resolving the ambiguous binding site of quercetin at the calcineurin subunit junction using funnel metadynamics with deep learning collective variables | bio | metadynamics, funnel metadynamics, DeepTICA | Jason Loo | ENERGY COM METAD FUNNEL COORDINATION LOWER_WALLS WHOLEMOLECULES WRAPAROUND DISTANCE PYTORCH_MODEL FUNNEL_PS RMSD MATHEVAL UPPER_WALLS PRINT GROUP | bias pytorch function core generic vatom funnel colvar |
| 26.001 | Molecular simulations Alx riboswitch | bio | RNA, riboswitch | Giovanni Bussi | ERMSD RESTRAINT DISTANCE MOLINFO MOVINGRESTRAINT MATHEVAL PRINT | function colvar bias generic |
| 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 | SAXS METAD INCLUDE GYRATION WHOLEMOLECULES CENTER DISTANCE MOLINFO MOVINGRESTRAINT UPPER_WALLS PRINT GROUP | bias isdb core generic vatom colvar |
| 25.017 | Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity | bio | EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase | Samuel Hoff | WHOLEMOLECULES BIASVALUE MOLINFO EMMIVOX PRINT GROUP | isdb bias generic core |
| 25.015 | Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY | materials | Molecular crystal, Force Field, Collective Variable | Pradip Si and Omar Valsson | TORSIONS DUMPMULTICOLVAR PRINT DISTANCES SMAC | generic symfunc multicolvar |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | MATHEVAL LOWER_WALLS MULTI_RMSD DISTANCE PBMETAD UPPER_WALLS PRINT UNITS RESTART | bias setup function generic 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 | METAD PUCKERING RESTRAINT DISTANCE MOLINFO MOVINGRESTRAINT RESTART PRINT TORSION | setup colvar bias generic |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | ALPHABETA RDC WHOLEMOLECULES FLUSH DISTANCE ENSEMBLE STATS MOLINFO METAINFERENCE PRINT GROUP | function isdb multicolvar core generic colvar |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | COORDINATION METAD CENTER DISTANCE RMSD GROUP CONTACTMAP ENERGY INCLUDE OPES_METAD_EXPLORE FLUSH FIXEDATOM BIASVALUE PYTORCH_MODEL FIT_TO_TEMPLATE MATHEVAL PRINT CUSTOM COMBINE LOWER_WALLS MOLINFO POSITION UPPER_WALLS OPES_METAD UNITS WHOLEMOLECULES ENDPLUMED | bias setup pytorch function core generic vatom opes colvar |
| 24.021 | Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state | chemistry | ion pairing, caco3, opes, proton transfer, crystallization | Pablo Piaggi | ENERGY COORDINATION DISTANCE UPPER_WALLS PRINT OPES_METAD | colvar bias generic opes |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | COM METAD DISTANCES WHOLEMOLECULES FLUSH CENTER DISTANCE CUSTOM POSITION PRINT UNITS GROUP | bias setup function multicolvar core generic vatom colvar |
| 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 | METAD CONSTANT LOWER_WALLS WHOLEMOLECULES CENTER DISTANCE BIASVALUE MATHEVAL UPPER_WALLS PRINT | bias function generic vatom colvar |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | COMBINE METAD ALPHARMSD WHOLEMOLECULES FIT_TO_TEMPLATE POSITION MOLINFO ANN PRINT | bias function annfunc secondarystructure generic colvar |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | PBMETAD LOAD PRINT PINES | setup bias generic pines |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | PATHMSD DRR METAD LOWER_WALLS FLUSH BIASVALUE CUSTOM UPPER_WALLS PRINT | bias function generic drr colvar |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | PRINT GYRATION WHOLEMOLECULES MOLINFO PBMETAD TORSION GROUP | colvar bias generic core |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | COMBINE Q4 Q6 LOCAL_Q4 LOCAL_Q6 MFILTER_MORE MFILTER_LESS CLUSTER_NATOMS COORDINATIONNUMBER DFSCLUSTERING LOCAL_AVERAGE PRINT GROUP CONTACT_MATRIX | clusters function adjmat multicolvar core generic symfunc |
| 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 | COM COORDINATION GROUP WHOLEMOLECULES BIASVALUE MOLINFO EMMI RMSD PBMETAD UPPER_WALLS PRINT RESTART TORSION | bias setup isdb core generic vatom colvar |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | COMBINE COM METAD REWEIGHT_BIAS INCLUDE GYRATION CONVERT_TO_FES DUMPGRID PRINT DISTANCES GROUP HISTOGRAM | bias function multicolvar core generic vatom colvar gridtools |
| 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 METAD BF_GAUSSIANS OPT_AVERAGED_SGD DISTANCE OPT_ADAM BF_CUBIC_B_SPLINES ENERGY BF_LEGENDRE INCLUDE FLUSH TD_WELLTEMPERED PRINT VES_OUTPUT_BASISFUNCTIONS TD_UNIFORM BF_CHEBYSHEV VES_LINEAR_EXPANSION POSITION UPPER_WALLS UNITS BF_WAVELETS | bias ves setup generic colvar |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | CONTACTMAP RANDOM_EXCHANGES ALPHARMSD METAD COORDINATION INCLUDE ANTIBETARMSD CENTER DISTANCE MOLINFO PRINT UNITS | bias setup secondarystructure generic vatom colvar |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | COMBINE METAD CONSTANT LOAD LOWER_WALLS RESTRAINT ENSEMBLE CUSTOM MOVINGRESTRAINT UPPER_WALLS PRINT UNITS TORSION | bias setup function generic colvar |
| 21.041 | Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics | methods | metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions | Matej Badin | COMBINE COORDINATION METAD ENDPLUMED VOLUME CUSTOM PRINT | colvar function generic bias |
| 21.015 | Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin | bio | metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module | Gaston Courtade | COORDINATION METAD REWEIGHT_BIAS PRINT WHOLEMOLECULES CENTER RESTRAINT POSITION MATHEVAL RESTART | bias setup function generic vatom colvar |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | ECV_UMBRELLAS_LINE ECV_MULTITHERMAL VOLUME ENVIRONMENTSIMILARITY RMSD ECV_MULTITHERMAL_MULTIBARIC Q6 ENERGY ECV_LINEAR LOAD MATHEVAL PRINT CUSTOM MOLINFO POSITION UPPER_WALLS TORSION UNITS ENDPLUMED WHOLEMOLECULES OPES_EXPANDED | bias setup function envsim symfunc opes generic colvar |
| 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 | CONTACTMAP COM PROJECTION_ON_AXIS METAD CONSTANT INCLUDE FUNCPATHGENERAL LOAD WHOLEMOLECULES LOWER_WALLS DISTANCE BIASVALUE MOLINFO MATHEVAL UPPER_WALLS PRINT GROUP | bias setup function core generic vatom colvar |
| 19.046 | Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding | bio | VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation | Faidon Brotzakis | COMBINE COM ALPHABETA FUNNEL METAD LOWER_WALLS WHOLEMOLECULES REWEIGHT_METAD DISTANCE MOLINFO RMSD BRIDGE UPPER_WALLS PRINT DISTANCES GROUP TORSION | bias function adjmat multicolvar core vatom generic funnel colvar |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | CONTACTMAP COM METAD FUNCPATHMSD WHOLEMOLECULES ENDPLUMED DISTANCE RMSD PRINT | bias function vatom generic colvar |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | COMBINE ALPHABETA COMMITTOR METAD FLUSH MOLINFO PRINT | function generic bias multicolvar |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | CS2BACKBONE RDC WHOLEMOLECULES MOLINFO METAINFERENCE PRINT GROUP | isdb generic core |
| 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 | WHOLEMOLECULES DISTANCE PRINT ANGLE METAD | colvar bias generic |
| 26.000 | OPES simulations of disordered proteins | bio | OPES, IDPs | Julian Streit | OPES_EXPANDED PRINT ECV_MULTITHERMAL ENERGY RESTART | setup colvar opes generic |
| 25.020 | Revealing Water-Mediated Activation Mechanisms in the Beta 1-Adrenergic Receptor via OneOPES-Enhanced Free Energy Landscapes | bio | OneOPES, GPCR, ADRB1, activation, microswitches, conformational changes, allostery | Valerio Rizzi | GHOST GROUP DISTANCE OPES_EXPANDED RMSD PRINT CENTER OPES_METAD_EXPLORE PATHMSD LOWER_WALLS DISTANCES CUSTOM ECV_MULTITHERMAL UPPER_WALLS ENERGY COORDINATION | multicolvar core opes function colvar vatom bias 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 | COORDINATIONNUMBER GROUP DISTANCE FIXEDATOM PRINT ZDISTANCES DISTANCES UNITS FLUSH OPES_METAD CUSTOM COMMITTOR UPPER_WALLS | multicolvar core symfunc opes function colvar setup vatom bias generic |
| 24.018 | A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations | chemistry | prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning | Léon HUET | PRINT DISTANCE | colvar generic |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | WHOLEMOLECULES GROUP EMMIVOX PRINT INCLUDE ERMSD BIASVALUE RESTRAINT MOLINFO | isdb core generic bias colvar |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | WHOLEMOLECULES TORSION PRINT FLUSH METAD RESTART | setup colvar bias generic |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | DISTANCE FIXEDATOM TORSION PRINT CENTER MATHEVAL METAD CUSTOM UPPER_WALLS | function colvar vatom bias generic |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | WHOLEMOLECULES GROUP DISTANCE PRINT COORDINATION CENTER OPES_METAD_EXPLORE COM METAD CUSTOM UPPER_WALLS LOWER_WALLS | core opes function generic vatom bias colvar |
| 22.021 | Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn Løland Bore | ENVIRONMENTSIMILARITY OPES_EXPANDED PRINT INCLUDE ECV_UMBRELLAS_LINE UPPER_WALLS LOWER_WALLS | envsim opes bias generic |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | ENDPLUMED ECV_UMBRELLAS_FILE PBMETAD OPES_EXPANDED TORSION PRINT METAD OPES_METAD_EXPLORE UNITS BIASVALUE OPES_METAD CUSTOM ECV_MULTITHERMAL POSITION UPPER_WALLS ENERGY LOWER_WALLS | opes function generic setup bias colvar |
| 21.036 | Modelling the structure and interactions of intrinsically disordered peptides with multiple-replica, metadynamics-based sampling methods and force-field combinations | bio | Bias Exchange Metadynamics, PTWTE-metaD | Matteo Salvalaglio | WHOLEMOLECULES GROUP PARABETARMSD RANDOM_EXCHANGES PRINT COORDINATION ANTIBETARMSD GYRATION DIHCOR METAD ENERGY ALPHARMSD UPPER_WALLS MOLINFO LOWER_WALLS | multicolvar core secondarystructure generic bias colvar |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | COORDINATIONNUMBER CONVERT_TO_FES LOAD DUMPGRID PRINT MOVINGRESTRAINT UNITS FLUSH REWEIGHT_METAD METAD COMMITTOR UPPER_WALLS HISTOGRAM | gridtools symfunc setup bias generic |
| 21.002 | Phase equilibrium of water with hexagonal and cubic ice using the SCAN functional | materials | ice, water, SCAN, OPES, VES, multithermal, crystallization, environment similarity, refcv, reweighting | Pablo Piaggi | ENVIRONMENTSIMILARITY TD_UNIFORM OPES_EXPANDED ECV_MULTITHERMAL_MULTIBARIC PRINT MATHEVAL VOLUME Q6 VES_LINEAR_EXPANSION ECV_UMBRELLAS_LINE UPPER_WALLS BF_LEGENDRE OPT_AVERAGED_SGD ENERGY RESTART | ves symfunc opes function colvar envsim setup bias generic |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | COORDINATIONNUMBER ENDPLUMED GROUP PRINT EXTERNAL UNITS FLUSH METAD COMBINE RESTART | core symfunc function setup bias generic |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | ENDPLUMED GROUP DISTANCE TORSION PRINT CENTER ANGLE CUSTOM COMBINE DUMPDERIVATIVES RESTRAINT | core function generic vatom bias colvar |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | WHOLEMOLECULES ENDPLUMED DISTANCE LOWER_WALLS RESTRAINT COORDINATION | colvar bias generic |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | ANN COMBINE COM POSITION RESTRAINT | annfunc function vatom bias colvar |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | TORSION RANDOM_EXCHANGES PRINT INCLUDE METAD | generic bias colvar |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | CONTACT_MATRIX CLUSTER_NATOMS ENDPLUMED CLUSTER_WITHSURFACE OUTPUT_CLUSTER MFILTER_MORE LOCAL_Q6 FLUSH Q6 DFSCLUSTERING COMMITTOR | adjmat multicolvar clusters symfunc generic |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | TORSION CONSTANT INCLUDE MATHEVAL PUCKERING BIASVALUE MOLINFO | bias generic function colvar |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | WHOLEMOLECULES GROUP PBMETAD PRINT INCLUDE METAINFERENCE MOLINFO | isdb core bias generic |
| 26.006 | Metadynamics simulations of buried phosphorylation sites and proline isomerisation | bio | metadynamics | Julian Streit | WHOLEMOLECULES MOLINFO COORDINATION PRINT METAD TORSION | generic bias colvar |
| 25.029 | Energetic Constraints in the Enzymatic Depolymerization of Crystalline PET from enhanced molecular simulations | bio | HREX-Metadynamics, PETase, crystalline PET, amorphous PET, conformational ensembles, substrate binding, chain detachment | Ania Di Pede-Mattatelli and Francesco Colizzi | UPPER_WALLS REWEIGHT_BIAS COM FIXEDATOM WHOLEMOLECULES CONVERT_TO_FES LOWER_WALLS DISTANCE MOLINFO DUMPGRID HISTOGRAM PRINT METAD | bias generic vatom gridtools colvar |
| 25.014 | Atomic resolution ensembles of intrinsically disordered proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | GROUP PRINT BAIES BIASVALUE | generic bias core isdb |
| 25.005 | Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations | chemistry | WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD | Vikas Tiwari, Tarak Karmakar | GROUP ANGLE UPPER_WALLS COM RESTRAINT FIXEDATOM COMBINE FLUSH LOWER_WALLS DISTANCE DISTANCES COORDINATION UNITS PRINT METAD COORDINATIONNUMBER | bias generic core function multicolvar symfunc setup vatom colvar |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | ERMSD ECV_MULTITHERMAL RESTART COMBINE PYTORCH_MODEL OPES_EXPANDED MOLINFO VOLUME OPES_METAD_EXPLORE COORDINATION ENERGY PRINT | generic pytorch function setup opes colvar |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | FLUSH COORDINATION PRINT RMSD FIT_TO_TEMPLATE FIXEDATOM READ MATHEVAL HISTOGRAM COMMITTOR GROUP UPPER_WALLS WHOLEMOLECULES CONVERT_TO_FES PATH WRAPAROUND DUMPGRID CONTACTMAP INCLUDE COM REWEIGHT_METAD ENDPLUMED MOLINFO DISTANCE METAD | generic bias mapping core function vatom gridtools colvar |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | COMBINE MATHEVAL Q4 VOLUME Q6 ENERGY PRINT METAD COORDINATIONNUMBER | generic bias function symfunc 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 | CUSTOM FLUSH COORDINATION PRINT TORSION FIT_TO_TEMPLATE POSITION MATHEVAL COMMITTOR GROUP CENTER UPPER_WALLS WHOLEMOLECULES WRAPAROUND OPES_METAD_EXPLORE UNITS OPES_METAD BIASVALUE COM ENDPLUMED MOLINFO DISTANCE LOWER_WALLS ENERGY | generic bias core function setup vatom opes colvar |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | COMMITTOR GROUP UPPER_WALLS COM UNITS FIXEDATOM CUSTOM MATHEVAL FLUSH DISTANCE LOWER_WALLS DISTANCES ZDISTANCES ENERGY PRINT COORDINATIONNUMBER OPES_METAD | generic bias core function multicolvar symfunc setup vatom opes colvar |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | LOCAL_Q3 GROUP LOCAL_AVERAGE CLUSTER_NATOMS Q3 RESTRAINT AROUND FIXEDATOM CONTACT_MATRIX LOAD DENSITY DFSCLUSTERING DUMPGRID CLUSTER_DISTRIBUTION PRINT UNITS HISTOGRAM COORDINATIONNUMBER | bias generic volumes core symfunc adjmat clusters setup vatom gridtools |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | GROUP LOCAL_Q6 MOVINGRESTRAINT MFILTER_MORE COMBINE LOWER_WALLS Q6 PRINT METAD COORDINATIONNUMBER | bias generic core function symfunc multicolvar |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | PAIRENTROPY GROUP CENTER LOAD COMBINE MATHEVAL Q4 Q6 INCLUDE PRINT METAD COORDINATIONNUMBER | generic bias core function symfunc setup vatom gridtools |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | PRINT METAD DISTANCES DISTANCE | generic multicolvar bias colvar |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | GROUP UPPER_WALLS GYRATION WHOLEMOLECULES FLUSH LOWER_WALLS COORDINATION PRINT METAD | bias generic core colvar |
| 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 | COMMITTOR RMSD FIT_TO_TEMPLATE CENTER GROUP UPPER_WALLS FIXEDATOM WHOLEMOLECULES PYTORCH_MODEL MATHEVAL LOWER_WALLS DISTANCE CUSTOM COORDINATION PRINT OPES_METAD | generic bias pytorch core function vatom opes colvar |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | RMSD COM WHOLEMOLECULES COMBINE MOLINFO DISTANCE PRINT METAD COORDINATIONNUMBER COMMITTOR | generic bias function 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 | ANGLE UPPER_WALLS WHOLEMOLECULES ALPHABETA ALPHARMSD FLUSH MOLINFO DISTANCE COORDINATION PRINT METAD TORSION | bias generic secondarystructure multicolvar colvar |
| 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 UPPER_WALLS DISTANCE | bias generic colvar |
| 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 | REWEIGHT_TEMP_PRESS TD_WELLTEMPERED OPT_DUMMY RESTART PRINT OPT_AVERAGED_SGD CELL READ LOAD MATHEVAL BF_LEGENDRE TD_MULTITHERMAL_MULTIBARIC HISTOGRAM VES_LINEAR_EXPANSION UPPER_WALLS COMBINE CONVERT_TO_FES DUMPGRID Q6 REWEIGHT_BIAS LOWER_WALLS VOLUME ENERGY | bias generic function ves symfunc setup gridtools colvar |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | POSITION MAZE_LOSS UNITS PRINT MAZE_OPTIMIZER_BIAS MAZE_SIMULATED_ANNEALING | generic setup maze colvar |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | POSITION MAZE_LOSS UNITS PRINT MAZE_OPTIMIZER_BIAS MAZE_SIMULATED_ANNEALING | generic setup maze colvar |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | UPPER_WALLS CELL ENDPLUMED FCCUBIC UNITS PRINT METAD | bias generic symfunc setup colvar |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | UPPER_WALLS COMBINE FLUSH DISTANCE DISTANCES RESTART UNITS PRINT METAD | bias generic function setup multicolvar colvar |
| 19.041 | Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces | bio | metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption | Jim Pfaendtner | UPPER_WALLS COM DISTANCE ENERGY PRINT METAD | bias generic vatom colvar |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | PIV UPPER_WALLS FUNCPATHMSD LOWER_WALLS CELL PRINT METAD | bias generic function piv colvar |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | UPPER_WALLS COM WHOLEMOLECULES LOWER_WALLS DISTANCE PRINT METAD | bias generic vatom colvar |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | PRINT TORSION DRR | generic drr colvar |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | BIASVALUE GROUP WHOLEMOLECULES MOLINFO EMMI PRINT | bias generic core isdb |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | BIASVALUE GROUP MOLINFO EMMI PRINT | bias generic core isdb |
| 26.017 | Vasopressin V2 receptor phosphopeptide reshapes the conformational landscape of arrestin-2 beyond C-tail detachment | bio | Arrestin, GPCR, OneOPES, conformational changes, allostery | Simone Aureli | ECV_MULTITHERMAL CENTER UNITS COORDINATION LOWER_WALLS DISTANCE MOLINFO ANGLE INCLUDE PROJECTION_ON_AXIS TORSION MATHEVAL GROUP CUSTOM FUNCPATHMSD RMSD UPPER_WALLS OPES_EXPANDED COMBINE PRINT OPES_METAD_EXPLORE COM CONTACTMAP ENERGY LOAD | colvar opes core function setup generic bias vatom |
| 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 METAD FUNNEL_PS FUNNEL LOWER_WALLS PRINT COM | generic funnel bias vatom |
| 25.022 | Imidazole Diffusion in SALEM-2 MOF | materials | OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials | Sudheesh Kumar Ethirajan | OPES_METAD PROJECTION_ON_AXIS DISTANCES CENTER UNITS ENDPLUMED DISTANCE GROUP PRINT WHOLEMOLECULES MOLINFO | colvar opes multicolvar core setup generic vatom |
| 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 INCLUDE RESTART TORSION CENTER PBMETAD READ GYRATION ENERGY DUMPATOMS DISTANCE PRINT WHOLEMOLECULES MOLINFO VOLUME | colvar setup generic bias vatom |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | UPPER_WALLS ABMD UNITS ENDPLUMED PRINT PATHMSD | generic colvar bias setup |
| 24.033 | Transient interactions between the fuzzy coat and the cross-b core of brain-derived Ab42 filaments | bio | CryoEM, MEMMI, Metadynamics, Metainference, Ab42 Fibrils, structural ensemble | Maria Milanesi | UPPER_WALLS CENTER PBMETAD DUMPMASSCHARGE COORDINATION ALPHARMSD DISTANCE GROUP PARABETARMSD BIASVALUE PRINT WHOLEMOLECULES EMMI MOLINFO DUMPATOMS COM RMSD | colvar secondarystructure core isdb generic bias vatom |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | METAD RESTART TORSION PUCKERING PRINT MOLINFO | generic colvar bias setup |
| 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 | UPPER_WALLS OPES_METAD RESTART TORSION CENTER PYTORCH_MODEL COORDINATION LOWER_WALLS DISTANCE GROUP PATH CUSTOM FIXEDATOM WHOLEMOLECULES PRINT FIT_TO_TEMPLATE | mapping colvar opes core pytorch function setup generic 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 | METAD RESTRAINT RESTART COMMITTOR FLUSH TORSION ENERGY BIASVALUE DISTANCE PRINT MATHEVAL COORDINATIONNUMBER MOLINFO | symfunc colvar function setup generic bias |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | METAD UNITS COMBINE DISTANCE PRINT WHOLEMOLECULES | colvar function setup generic 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 | METAD GHBFIX COMBINE BIASVALUE COORDINATION PRINT ERMSD WHOLEMOLECULES MOLINFO | generic colvar function bias |
| 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 | UPPER_WALLS OPES_METAD TORSION CENTER UNITS PYTORCH_MODEL COORDINATION LOWER_WALLS DISTANCE PRINT GROUP CUSTOM PATH FIXEDATOM WHOLEMOLECULES OPES_METAD_EXPLORE FIT_TO_TEMPLATE | mapping colvar opes core pytorch function setup generic bias vatom |
| 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 | UPPER_WALLS METAD CONSTANT LOWER_WALLS DISTANCE MATHEVAL BIASVALUE PRINT WHOLEMOLECULES | generic colvar function 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 | COMMITTOR CENTER PYTORCH_MODEL COORDINATION LOWER_WALLS DISTANCE FIXEDATOM FIT_TO_TEMPLATE MOLINFO ANGLE INCLUDE MATHEVAL GROUP CUSTOM RMSD UPPER_WALLS OPES_METAD COMBINE PRINT WHOLEMOLECULES CONTACTMAP ENERGY ENDPLUMED | colvar opes core pytorch function generic bias vatom |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | UPPER_WALLS METAD RESTRAINT UNITS PAIRENTROPY LOCAL_AVERAGE ENERGY Q4 Q6 PRINT CUSTOM PIV FUNCPATHMSD VOLUME | symfunc colvar function setup generic gridtools bias piv |
| 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 METAD CONTACTMAP ENERGY LOWER_WALLS PRINT WHOLEMOLECULES | generic colvar bias |
| 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 METAD PCAVARS LOWER_WALLS PRINT WHOLEMOLECULES | mapping bias generic |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | METAD FLUSH UNITS DRR BIASVALUE DISTANCE PRINT CUSTOM COM | colvar drr function setup generic bias vatom |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | ANTIBETARMSD RESTART TORSION PBMETAD COM ALPHARMSD PRINT WHOLEMOLECULES MOLINFO ALPHABETA | colvar secondarystructure multicolvar setup generic bias vatom |
| 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 | UPPER_WALLS OPES_METAD RESTART AROUND ENERGY ENVIRONMENTSIMILARITY DUMPGRID PRINT CUSTOM VOLUME HISTOGRAM | colvar opes function setup generic gridtools bias envsim volumes |
| 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 | UPPER_WALLS METAD FLUSH UNITS GYRATION COMBINE COORDINATION LOWER_WALLS DISTANCE COORDINATIONNUMBER COM | symfunc colvar function setup generic bias vatom |
| 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 TORSION PRINT FIXEDATOM FIT_TO_TEMPLATE | generic colvar bias vatom |
| 21.040 | A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms | bio | EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference | Faidon Brotzakis | UPPER_WALLS RESTART COM BIASVALUE DISTANCE GROUP PRINT WHOLEMOLECULES EMMI MOLINFO | colvar core isdb setup generic bias vatom |
| 21.034 | Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics | bio | reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics | Dongdong Wang | METAD INCLUDE TORSION PBMETAD ENDPLUMED PRINT RANDOM_EXCHANGES | 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 | METAD INCLUDE TORSION UNITS CONSTANT ENERGY BIASVALUE DISTANCE REWEIGHT_METAD PRINT CUSTOM | colvar function setup generic bias |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | UPPER_WALLS METAD FUNNEL_PS FUNNEL LOWER_WALLS DISTANCE PRINT COM | colvar generic bias funnel vatom |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | UPPER_WALLS OPES_METAD FLUSH PYTORCH_MODEL LOWER_WALLS MATHEVAL GROUP PRINT LOAD | opes core pytorch function setup generic 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 | METAD RESTRAINT CONVERT_TO_FES MULTI_RMSD REWEIGHT_METAD DUMPGRID PRINT HISTOGRAM | generic gridtools bias colvar |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | UPPER_WALLS OPES_METAD CENTER ENERGY PYTORCH_MODEL COORDINATION ENDPLUMED DISTANCE GROUP MATHEVAL PRINT FIXEDATOM WHOLEMOLECULES FIT_TO_TEMPLATE ANGLE | colvar opes core pytorch function generic bias vatom |
| 20.014 | amyloid beta small molecule interaction | bio | intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta | Gabriella Heller | FLUSH GYRATION COORDINATION ALPHARMSD CS2BACKBONE METAINFERENCE MOLINFO INCLUDE PARABETARMSD GROUP ENSEMBLE PBMETAD COMBINE PRINT WHOLEMOLECULES DIHCOR ANTIBETARMSD ENDPLUMED STATS | colvar secondarystructure multicolvar core isdb function generic bias |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | DISTANCES RESTART CENTER COORDINATION DISTANCE GROUP PRINT WHOLEMOLECULES | colvar multicolvar core setup generic vatom |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | UPPER_WALLS METAD CENTER ENERGY COMBINE LOWER_WALLS DISTANCE PRINT MATHEVAL WHOLEMOLECULES MOLINFO RMSD | colvar function generic bias vatom |
| 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 | UPPER_WALLS METAD ABMD CONVERT_TO_FES READ ENDPLUMED COMBINE LOWER_WALLS DISTANCE PRINT MATHEVAL REWEIGHT_METAD DUMPGRID COM HISTOGRAM | colvar function generic gridtools bias vatom |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | METAD GYRATION ENERGY PRINT WHOLEMOLECULES | generic colvar bias |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | TORSION POSITION UNITS ENERGY ENDPLUMED ENVIRONMENTSIMILARITY Q6 PRINT LOAD | symfunc colvar setup generic envsim |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | UPPER_WALLS METAD FLUSH UNITS ENERGY COMBINE LOWER_WALLS DISTANCE PRINT | colvar function setup generic bias |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | UPPER_WALLS METAD FLUSH UNITS ENERGY COMBINE DISTANCE PRINT | colvar function setup generic bias |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | METAD GYRATION ENERGY ENDPLUMED ALPHARMSD PRINT WHOLEMOLECULES MOLINFO | generic colvar secondarystructure bias |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | UPPER_WALLS WRAPAROUND METAD FLUSH POSITION CONVERT_TO_FES READ ENDPLUMED COORDINATION REWEIGHT_METAD MATHEVAL GROUP PRINT DUMPGRID WHOLEMOLECULES FIT_TO_TEMPLATE COM HISTOGRAM | colvar core function generic gridtools bias vatom |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | BIASVALUE GROUP PRINT EMMI MOLINFO | generic isdb bias core |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | UPPER_WALLS METAD INCLUDE DISTANCES FLUSH COMBINE LOWER_WALLS DISTANCE PRINT RANDOM_EXCHANGES ERMSD MOLINFO ANGLE | colvar multicolvar function generic bias |
| 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 GROUP OPES_METAD_EXPLORE COORDINATION PRINT LOWER_WALLS CENTER LOAD BIASVALUE | vatom setup colvar bias core generic function opes |
| 26.007 | Metadynamics Simulations Reveal the Protonation-Dependent Conformational Landscape of GSK-3β Dual Inhibitors | chemistry | metadynamics, ligand unbinding, path CVs, funnel metadynamics | Gian Marco Elisi | FUNNEL COM PRINT METAD RMSD PATHMSD LOWER_WALLS UPPER_WALLS FUNNEL_PS ENDPLUMED ANGLE WHOLEMOLECULES MATHEVAL DISTANCE UNITS MOLINFO COMBINE | vatom setup colvar bias funnel generic function |
| 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 | GHOST GROUP OPES_METAD_EXPLORE COORDINATION PRINT MOLINFO ECV_MULTITHERMAL RMSD CENTER ENERGY DISTANCE CUSTOM OPES_EXPANDED COMBINE | vatom colvar core generic function opes |
| 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 | BAIES BIASVALUE GROUP PRINT | generic isdb core bias |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | PRINT RESTRAINT DISTANCE GYRATION PYTORCH_MODEL | bias colvar pytorch generic |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | GROUP GHOST PRINT METAD POSITION LOWER_WALLS DISTANCES CENTER UPPER_WALLS PUCKERING WHOLEMOLECULES MATHEVAL DISTANCE GYRATION MOLINFO SORT COMBINE | vatom colvar bias core generic function multicolvar |
| 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 | GROUP METAD PRINT LOAD COMMITTOR TORSION | setup colvar bias core generic |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | COORDINATION PRINT LOWER_WALLS UPPER_WALLS MATHEVAL WHOLEMOLECULES UNITS GROUP RMSD ENDPLUMED LOAD INCLUDE DISTANCE MOLINFO POSITION CELL ENERGY BIASVALUE TORSION CUSTOM | setup colvar bias core generic function |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | COM MOVINGRESTRAINT PRINT METAD LOWER_WALLS UPPER_WALLS WHOLEMOLECULES DISTANCE ANGLE | vatom generic colvar bias |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | METAD TORSION PRINT | generic colvar bias |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | ECV_MULTITHERMAL PRINT POSITION OPES_METAD ENDPLUMED ENERGY UNITS OPES_EXPANDED TORSION | colvar opes setup generic |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | OPES_METAD_EXPLORE PRINT COORDINATION UNITS CUSTOM PYTORCH_MODEL | pytorch setup colvar generic function opes |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | GHBFIX GROUP BIASVALUE METAD COORDINATION MOLINFO PRINT UPPER_WALLS LOAD FLUSH CUSTOM COMBINE | setup bias colvar core generic function |
| 22.035 | Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties | bio | intrinsically disordered proteins, parallel bias metadynamics, protein | Kresten Lindorff-Larsen | WHOLEMOLECULES GYRATION MOLINFO PBMETAD TORSION | bias colvar generic |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | COM PRINT UPPER_WALLS DISTANCE GYRATION MOLINFO PBMETAD | vatom colvar generic bias |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | EMMIVOX GROUP PRINT MOLINFO LOAD WHOLEMOLECULES BIASVALUE | isdb setup bias core generic |
| 21.048 | Enhancing ligand exploration within a channel pore and fenestrations using metadynamics | bio | well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug | Elaine Tao | COM PRINT METAD LOWER_WALLS UPPER_WALLS DISTANCE UNITS CUSTOM TORSION | vatom setup colvar bias generic function |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | OPT_AVERAGED_SGD PRINT METAD RESTART TD_WELLTEMPERED ENERGY LOAD VES_LINEAR_EXPANSION VOLUME PAIRENTROPY BF_LEGENDRE COMBINE | setup bias colvar generic ves function gridtools |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | COM PRINT UPPER_WALLS DISTANCE GYRATION MOLINFO PBMETAD | vatom colvar generic bias |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | PRINT OPES_METAD Q6 WHOLEMOLECULES UNITS CONTACTMAP GROUP RMSD ENDPLUMED LOAD INCLUDE DISTANCE VOLUME MOLINFO FLUSH OPES_EXPANDED ENVIRONMENTSIMILARITY ENERGY TORSION PYTORCH_MODEL ECV_MULTITHERMAL COMBINE | pytorch setup colvar symfunc core generic function opes envsim |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | GROUP COORDINATION WHOLEMOLECULES UNITS PBMETAD | setup colvar bias core generic |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | GROUP PRINT METAD MOLINFO LOWER_WALLS ERMSD UPPER_WALLS GYRATION WHOLEMOLECULES INCLUDE SAXS CUSTOM | isdb bias colvar core generic function |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | AROUND GROUP FIXEDATOM CONTACT_MATRIX PRINT CLUSTER_DISTRIBUTION RESTRAINT CLUSTER_NATOMS COORDINATIONNUMBER DUMPGRID DENSITY LOAD MFILTER_MORE DFSCLUSTERING MULTICOLVARDENS | vatom adjmat multicolvar setup bias symfunc volumes core generic gridtools clusters |
| 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 | PRINT METAD LOWER_WALLS RESTART PATHMSD UPPER_WALLS WHOLEMOLECULES | bias colvar setup generic |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | COM GROUP PRINT WHOLEMOLECULES DISTANCE | vatom core colvar 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 | METAD DISTANCE TORSION PRINT | generic colvar bias |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | GROUP PRINT LOWER_WALLS DISTANCES UPPER_WALLS ENERGY LOAD DISTANCE UNITS TORSION COMBINE | setup bias colvar core generic function multicolvar |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | GROUP PRINT METAD CENTER UPPER_WALLS LOAD INCLUDE VOLUME | vatom setup bias colvar core generic |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | GROUP PRINT CENTER ENDPLUMED INCLUDE DISTANCE | vatom core 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 | GROUP COORDINATION PRINT METAD POSITION LOWER_WALLS RESTART UPPER_WALLS UNITS FLUSH | setup colvar bias core generic |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | PRINT METAD RMSD ERMSD ENDPLUMED WHOLEMOLECULES MOLINFO | bias colvar generic |
| 26.014 | Dissociation free energy (DFE) calculationsfor GPR15L–polySia | bio | metadynamics, protein-carbohydrate interaction | Davide Luciano and Gaston Courtade | PRINT COM DISTANCE UPPER_WALLS METAD GROUP | vatom bias generic core colvar |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | TORSION METAINFERENCE STATS PRINT DISTANCE UPPER_WALLS MOLINFO GYRATION SAXS FLUSH WHOLEMOLECULES PBMETAD CENTER ENSEMBLE | vatom bias isdb function generic colvar |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | MOLINFO ERMSD COMBINE METAD WHOLEMOLECULES | generic bias colvar 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 UNITS COORDINATION PRINT DISTANCE RESTART UPPER_WALLS CUSTOM COMMITTOR LOWER_WALLS GROUP | opes bias function setup generic core colvar |
| 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 | COORDINATIONNUMBER OPES_METAD UNITS DISTANCE PRINT UPPER_WALLS ZDISTANCES FLUSH FIXEDATOM GROUP | vatom opes bias multicolvar symfunc setup generic core colvar |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | PRINT COM DISTANCE UPPER_WALLS MOLINFO GYRATION PBMETAD LOWER_WALLS | vatom generic bias colvar |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | PRINT COM DISTANCE UPPER_WALLS GYRATION PBMETAD | vatom generic bias colvar |
| 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 | CONVERT_TO_FES RMSD PRINT DISTANCE READ MOLINFO REWEIGHT_METAD MATHEVAL METAD WHOLEMOLECULES HISTOGRAM DUMPGRID | gridtools bias function generic colvar |
| 23.003 | Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations | methods | metadynamics, alchemical variable, alchemical free energy calculations | Wei-Tse Hsu | TORSION PRINT READ EXTRACV METAD | generic bias colvar |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | OPES_EXPANDED ECV_UMBRELLAS_LINE PRINT UPPER_WALLS INCLUDE ENVIRONMENTSIMILARITY RESTART LOWER_WALLS | opes bias envsim setup generic |
| 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 DRR PRINT BIASVALUE METAD FLUSH CUSTOM | drr bias function generic colvar |
| 22.027 | Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain | Max Bonomi | RMSD PRINT | generic colvar |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | COORDINATIONNUMBER CONVERT_TO_FES ANN UNITS MOVINGRESTRAINT PRINT VOLUME UPPER_WALLS BIASVALUE FLUSH CUSTOM REWEIGHT_BIAS HISTOGRAM COMMITTOR RESTRAINT LOAD DUMPGRID | gridtools bias function symfunc annfunc setup generic colvar |
| 22.020 | Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA | bio | RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics | Weiwei He | TORSION PRINT COM DISTANCE METAD WHOLEMOLECULES GROUP | vatom bias generic core colvar |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | WHOLEMOLECULES ANGLE ENERGY FIT_TO_TEMPLATE COORDINATION DISTANCE UPPER_WALLS PRINT GROUP MATHEVAL FLUSH ENDPLUMED CENTER COMMITTOR FIXEDATOM LOAD PYTORCH_MODEL | vatom bias pytorch function setup generic core colvar |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | COORDINATIONNUMBER ENERGY PRINT GROUP INCLUDE VOLUME METAD COMBINE CENTER LOAD | vatom bias symfunc function setup generic core colvar |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | UNITS PRINT COM DISTANCE UPPER_WALLS METAD WHOLEMOLECULES LOWER_WALLS | vatom bias setup generic colvar |
| 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 | TORSION ENERGY COORDINATION DISTANCE COM GYRATION INCLUDE PRINT ALPHABETA METAD PBMETAD | vatom bias generic multicolvar colvar |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | TORSION ENERGY PRINT MOLINFO EXTERNAL FLUSH RESTART | setup generic bias colvar |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | ANGLE COORDINATION DISTANCE DISTANCES MATHEVAL ENDPLUMED FIXEDATOM LOAD LOWER_WALLS TORSION OPES_METAD UNITS UPPER_WALLS WHOLEMOLECULES PYTORCH_MODEL PRINT CENTER FIT_TO_TEMPLATE GROUP | vatom opes bias multicolvar pytorch function setup generic core colvar |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | ALPHARMSD CONTACTMAP ENERGY PRINT DISTANCE INCLUDE MOLINFO UPPER_WALLS MATHEVAL METAD WHOLEMOLECULES LOWER_WALLS | secondarystructure bias function generic colvar |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | OPT_AVERAGED_SGD DISTANCE COORDINATION BF_CHEBYSHEV DISTANCES METAD VES_LINEAR_EXPANSION UWALLS FLUSH HISTOGRAM RESTRAINT LOAD ANGLES LOWER_WALLS COORDINATIONNUMBER CONVERT_TO_FES UNITS UPPER_WALLS TD_GRID REWEIGHT_METAD DUMPGRID PRINT COMBINE EXTERNAL REWEIGHT_BIAS | ves gridtools bias multicolvar symfunc function setup generic colvar |
| 21.010 | Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry | chemistry | Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis | Théo Magrino | generic | |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | ALPHARMSD EEFSOLV METAINFERENCE PRINT MOLINFO BIASVALUE GYRATION SAXS FLUSH WHOLEMOLECULES PBMETAD CENTER GROUP | vatom secondarystructure bias isdb generic core colvar |
| 20.034 | Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations | bio | RNA, SARS-CoV-2, partial tempering | Sandro Bottaro | TORSION PRINT DISTANCE ABMD MOLINFO ERMSD CENTER RESTART | vatom bias setup generic colvar |
| 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 PRINT COORDINATION MOLINFO COMBINE WHOLEMOLECULES RESTRAINT | generic bias colvar function |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | UNITS MOVINGRESTRAINT PRINT GYRATION ENDPLUMED | setup generic bias colvar |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | TORSION RMSD PRINT DISTANCE ERMSD MOLINFO METAD WHOLEMOLECULES | generic bias colvar |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | MULTICOLVARDENS FIND_CONTOUR_SURFACE UNITS MORE_THAN CENTER FCCUBIC FOURIER_TRANSFORM GROUP DUMPGRID | vatom gridtools fourier contour symfunc function setup core |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | FUNNEL_PS RMSD DISTANCE COM UPPER_WALLS PRINT METAD FUNNEL WHOLEMOLECULES LOWER_WALLS | vatom bias funnel generic colvar |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | UNITS PRINT DISTANCE UPPER_WALLS MATHEVAL METAD FLUSH RESTART | bias function setup generic colvar |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | PRINT GROUP UPPER_WALLS MOLINFO GYRATION ALPHABETA METAD WHOLEMOLECULES LOWER_WALLS | bias generic multicolvar core colvar |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | TORSION PRINT DISTANCE COMBINE EDS RESTRAINT | bias eds function generic colvar |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | TORSION PRINT BIASVALUE METAD MATHEVAL WHOLEMOLECULES CONSTANT | generic bias colvar function |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | TORSION PRINT DISTANCE UPPER_WALLS METAD CENTER COMMITTOR LOWER_WALLS | vatom generic bias colvar |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | COORDINATIONNUMBER PRINT GYRATION DISTANCES METAD ENDPLUMED RESTART | bias symfunc setup generic multicolvar colvar |