Browse the eggs in PLUMED-NEST

PLUMED-NEST provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation or analysis contained in a published paper. Furthermore, PLUMED-NEST monitors the compatibility of the provided PLUMED input files with the current and development versions of the code and integrates links from these files to the PLUMED manual.

Here is the list of projects already deposited in PLUMED-NEST, while a complete bibliography can be found here.

plumID Name Category Keywords Contributor Actions Modules
25.004 Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride chemistry OPES, OPES flooding, Catalysis, Ammonia Synthesis Axel Tosello Gardini COMMITTOR OPES_METAD DISTANCES ZDISTANCES MEAN UNITS FIXEDATOM GROUP CUSTOM MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER FLUSH DISTANCE CONTACT_MATRIX PRINT UPPER_WALLS ONES SUM core bias vatom function colvar matrixtools symfunc setup multicolvar generic adjmat opes
24.034 Umbrella sampling of ion in transporter SLC26A7 bio umbrella sampling, transporter, ions Xiaoli Lu PRINT POSITION RESTRAINT UNITS bias colvar generic setup
24.002 Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes chemistry metadynamics, ligand design, solvent extraction Xiaoyu Wang RESTART METAD UNITS PRINT TORSION bias colvar generic setup
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 OPES_METAD_EXPLORE COORDINATION GROUP FIT_TO_TEMPLATE FIXEDATOM CONSTANT UNITS CUSTOM DISTANCE PYTORCH_MODEL UPPER_WALLS OPES_METAD LOWEST PRINT SUM EUCLIDEAN_DISTANCE LOWER_WALLS WHOLEMOLECULES COMBINE CENTER PDB2CONSTANT TORSION PATH core bias refdist vatom function colvar pytorch setup generic mapping opes
23.014 Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 bio metadynamics, oligomerization, chemokine receptors, GPCR, membrane Vittorio Limongelli METAD COM FLUSH DISTANCE WHOLEMOLECULES PRINT COMBINE UPPER_WALLS TORSION bias vatom function colvar generic
23.008 PBMetaD simulations of Histatin5 bio metadynamics, IDP, Rg, PPII Francesco Pesce GROUP GYRATION WHOLEMOLECULES PRINT PBMETAD MOLINFO TORSION core bias colvar generic
23.001 Quantum phase diagram of water chemistry Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella Sigbjørn-Løland Bore RESTART LOWER_WALLS ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE MORE_THAN MEAN ONES GROUP CUSTOM MATRIX_VECTOR_PRODUCT PRINT UPPER_WALLS OPES_EXPANDED INCLUDE SUM DISTANCE_MATRIX core bias function envsim matrixtools setup generic adjmat opes
22.040 From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure bio SARS-CoV-2, Spike, Omicron Miłosz Wieczór RMSD LOWER_WALLS CONSTANT SELECT_COMPONENTS METAD CUSTOM MATRIX_VECTOR_PRODUCT BIASVALUE WHOLEMOLECULES PCAVARS PRINT UPPER_WALLS COMBINE SUM bias function colvar valtools matrixtools generic mapping
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 COMMITTOR LOWER_WALLS MATHEVAL CONSTANT METAD CUSTOM DISTANCE PRINT UPPER_WALLS DRMSD CELL SUM function bias colvar generic
22.028 N-glycan conformer distributions in atomistic simulation bio REST2, RECT, N-glycan, pucker Isabell Grothaus METAD DUMPGRID PUCKERING PRINT CONVERT_TO_FES HISTOGRAM READ MOLINFO TORSION bias colvar generic gridtools
22.009 Glycosylation in calixarenes capsule chemistry Metadynamics, glycosylation, supramolecular catalysis GiovanniMaria Piccini COORDINATION BRIDGE ANGLE MEAN GROUP FIT_TO_TEMPLATE RMSD UNITS BRIDGE_MATRIX FLUSH DISTANCE UPPER_WALLS MATHEVAL DISTANCES PRINT LOWER_WALLS METAD WHOLEMOLECULES COMBINE SUM core bias function colvar setup multicolvar generic adjmat
22.003 Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling methods opes, metadynamics, reweighting, alanine, muller Michele Invernizzi OPES_METAD_EXPLORE OPES_METAD LOWER_WALLS METAD UNITS ECV_MULTITHERMAL CUSTOM BIASVALUE PRINT ENERGY PBMETAD POSITION UPPER_WALLS OPES_EXPANDED ENDPLUMED TORSION ECV_UMBRELLAS_FILE bias function colvar setup generic opes
21.050 N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity methods bio Isabell Louise Grothaus PRINT CENTER DISTANCE colvar generic vatom
21.019 Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations materials Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen Matteo Salvalaglio MATHEVAL COM TORSIONS DISTANCE KDE PRINT vatom function colvar gridtools multicolvar generic
21.016 MD SAXS GTPase associated center bio metadynamics, RNA, folding, SAXS Giovanni Bussi LOWER_WALLS SAXS METAD ERMSD GROUP GYRATION CUSTOM WHOLEMOLECULES PRINT UPPER_WALLS MOLINFO INCLUDE core bias isdb function colvar generic
21.005 Crystallization Collective Variable methods Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA Tarak Karmakar OPES_METAD MATHEVAL LOWER_WALLS GROUP FLUSH LOAD PYTORCH_MODEL PRINT UPPER_WALLS core bias function pytorch setup generic opes
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 RESTART LOWER_WALLS METAD WHOLEMOLECULES PRINT UPPER_WALLS PATHMSD bias colvar generic setup
20.032 Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil materials clustering, conformational isomers Matteo Salvalaglio PRINT TORSION ENDPLUMED colvar generic
20.019 Systematic finite-temperature reduction of crystal energy landscapes materials crystals, organics, structure prediction Matteo Salvalaglio LOWER_WALLS MATHEVAL METAD ENERGY UPPER_WALLS PRINT CELL VOLUME function bias colvar generic
20.013 Improving accuracy of biased Alchemistic simulations methods flying Gaussian method, Alchemistic simulations, thermodynamic integration, reweighting Vojtech Spiwok PRINT METAD TORSION bias colvar generic
20.004 Data-driven collective variables for enhanced sampling methods collective variables, machine learning, deep-lda Luigi Bonati OPES_METAD MATHEVAL LOWER_WALLS UNITS COM GROUP FLUSH DISTANCE PYTORCH_MODEL LOAD PRINT UPPER_WALLS ENDPLUMED TORSION core bias vatom function colvar pytorch setup generic opes
19.081 Calculation of phase diagrams in the multithermal-multibaric ensemble methods VES, variationally enhanced sampling, multithermal-multibaric, energy, Wang Landau, RefCV, kernel, bcc, fcc, sodium, aluminum Pablo Piaggi RESTART Q6 LOAD DUMPGRID CONVERT_TO_FES HISTOGRAM REWEIGHT_TEMP_PRESS CELL VES_LINEAR_EXPANSION ENERGY UPPER_WALLS VOLUME MATHEVAL BF_LEGENDRE TD_MULTITHERMAL_MULTIBARIC OPT_AVERAGED_SGD PRINT OPT_DUMMY LOWER_WALLS TD_WELLTEMPERED COMBINE READ REWEIGHT_BIAS bias function colvar ves symfunc gridtools setup generic
19.080 Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium methods ves, variationally enhanced sampling, vibrational excitation, chemical reactions Kristof Bal LOWER_WALLS COORDINATION ANGLE UNITS TD_WELLTEMPERED BF_CHEBYSHEV TD_GRID FLUSH DISTANCE EXTERNAL OPT_AVERAGED_SGD PRINT UPPER_WALLS COMBINE HISTOGRAM CONVERT_TO_FES DUMPGRID VES_LINEAR_EXPANSION bias function colvar ves gridtools setup generic
19.060 Neural networks-based variationally enhanced sampling methods ves, neural networks Luigi Bonati ENVIRONMENTSIMILARITY UNITS Q6 LOAD PRINT POSITION ENERGY ENDPLUMED TORSION envsim colvar symfunc setup generic
19.043 Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) methods metadynamics, chemistry, HLDA GiovanniMaria Piccini RESTART DISTANCES UNITS METAD FLUSH DISTANCE PRINT UPPER_WALLS COMBINE bias function colvar setup multicolvar generic
19.031 Ice nucleation using PIV-based path coordinates materials phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics Silvio Pipolo LOWER_WALLS METAD PRINT PIV UPPER_WALLS CELL FUNCPATHMSD bias function colvar piv generic
19.020 PTMetaD-WTE simulation of the Ntail IDP bio metadynamics, IDPs, protein folding Mattia Bernetti LESS_THAN METAD SECONDARY_STRUCTURE_RMSD GYRATION WHOLEMOLECULES ENERGY PRINT MOLINFO ALPHARMSD ENDPLUMED SUM bias function colvar secondarystructure generic
19.011 Automatic Gradient Computation for Collective Variables other gradient, differentiation, curvature Toni Giorgino ENDPLUMED generic
19.009 RNA tetraloops folding bio metadynamics, RNA, folding Giovanni Bussi RMSD METAD ERMSD WHOLEMOLECULES PRINT MOLINFO ENDPLUMED bias colvar generic
19.008 anncolvar methods neural network, dimensionality reduction Vojtech Spiwok LESS_THAN MATHEVAL METAD SECONDARY_STRUCTURE_RMSD WHOLEMOLECULES POSITION COMBINE PRINT ALPHARMSD FIT_TO_TEMPLATE MOLINFO SUM bias function colvar secondarystructure generic
19.007 EMMI Microtubules bio metainference, cryo-EM Max Bonomi GROUP BIASVALUE WHOLEMOLECULES PRINT EMMI MOLINFO core bias generic isdb
19.001 RNA SHAPE bio metadynamics, RNA, ligand binding Giovanni Bussi RANDOM_EXCHANGES LOWER_WALLS ANGLE DISTANCES METAD ERMSD FLUSH DISTANCE LOWEST PRINT COMBINE UPPER_WALLS MOLINFO INCLUDE bias function colvar multicolvar generic
25.000 Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer bio metadynamics, pathCV Sahithya Sridharan Iyer PRINT GROUP UPPER_WALLS METAD RESTART FUNCPATHGENERAL MOLINFO COM WHOLEMOLECULES DISTANCE function generic vatom bias core colvar setup
24.031 DeepLNE methods PATHCV, OPES, OneOPES Thorben Fröhlking PRINT VOLUME COMBINE COORDINATION ENERGY RESTART PYTORCH_MODEL MOLINFO OPES_EXPANDED ECV_MULTITHERMAL ERMSD OPES_METAD_EXPLORE function generic pytorch opes colvar setup
24.006 Water vapor condensation chemistry metadynamics, homogeneous condensation, chemical potential Shenghui Zhong SUM PRINT CLUSTER_PROPERTIES GROUP LESS_THAN METAD CONTACT_MATRIX COORDINATIONNUMBER DFSCLUSTERING UNITS MATRIX_VECTOR_PRODUCT MEAN ONES CLUSTER_NATOMS UPPER_WALLS function setup generic clusters adjmat symfunc core matrixtools bias
23.045 Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state bio Path CVs Metadynamics, GPCRs activation transition Vittorio Limongelli CONTACTMAP SUM PRINT INCLUDE LESS_THAN PATHMSD LOWER_WALLS UPPER_WALLS METAD MOLINFO ALPHARMSD SECONDARY_STRUCTURE_RMSD FUNCPATHMSD DISTANCE function generic secondarystructure colvar bias
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 SUM PRINT INCLUDE FLUSH METAD MATHEVAL SELECT_COMPONENTS valtools function generic matrixtools 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 PRINT COMBINE COORDINATION METAD GHBFIX MOLINFO BIASVALUE ERMSD WHOLEMOLECULES generic function colvar bias
23.025 Probing ion binding to G-quadruplexes and related events chemistry metadynamics, repulsive potential, nucleic acids, G-quadruplexes Marcelo Poleto PRINT POSITION FIT_TO_TEMPLATE GROUP WRAPAROUND LOWEST LOWER_WALLS UPPER_WALLS METAD DUMPATOMS DISTANCES FLUSH UNITS RESTART COM MATHEVAL WHOLEMOLECULES DISTANCE function setup generic multicolvar vatom core colvar bias
22.045 Binding mode and mechanism of enzymatic polyethylene terephthalate degradation bio metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation Francesco Colizzi MOVINGRESTRAINT PRINT LOWER_WALLS METAD COM WHOLEMOLECULES ANGLE UPPER_WALLS DISTANCE generic colvar vatom bias
22.043 Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES bio OPES, RNA, Tetraloop, Folding Gül Zerze CONTACTMAP PRINT ENERGY ECV_UMBRELLAS_LINE OPES_EXPANDED ECV_MULTITHERMAL WHOLEMOLECULES generic colvar opes
22.041 Skipping the Replica Exchange Ladder with Normalizing Flows methods OPES, alanine, normalizing flows, replica exchange Michele Invernizzi PRINT POSITION ENERGY UNITS TORSION OPES_EXPANDED OPES_METAD ECV_MULTITHERMAL ENDPLUMED generic colvar setup opes
22.038 Enhanced Sampling Aided Design of Molecular Photoswitches chemistry reaction discovery, OPES explore, graph CV Umberto Raucci PRINT PYTORCH_MODEL UNITS CUSTOM COORDINATION OPES_METAD_EXPLORE function generic pytorch opes colvar setup
22.027 Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes bio SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain Max Bonomi PRINT RMSD generic colvar
22.002 GAMBES_SAMPL5_RATES other GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding Jayashrita Debnath FIXEDATOM PRINT GROUP COMMITTOR FLUSH ENERGY UPPER_WALLS PYTORCH_MODEL ENDPLUMED CENTER LOAD MATHEVAL WHOLEMOLECULES ANGLE COORDINATION FIT_TO_TEMPLATE DISTANCE function setup generic vatom pytorch core colvar bias
21.046 Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs bio wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder Elena Papaleo SUM PRINT GROUP LOWER_WALLS COMBINE GYRATION UPPER_WALLS METAD ALPHABETA TORSION CONSTANT CUSTOM ENDPLUMED WHOLEMOLECULES function generic multicolvar core colvar bias
21.044 NaCl nucleation chemistry metadynamics, DFS clustering Aaron Finney SUM GROUP HISTOGRAM METAD MORE_THAN MEAN CUSTOM FIXEDATOM PRINT Q6 CLUSTER_DISTRIBUTION CONTACT_MATRIX COORDINATIONNUMBER DFSCLUSTERING DUMPGRID MFILTER_MORE COMBINE LOCAL_Q6 INSPHERE MATRIX_VECTOR_PRODUCT ONES CLUSTER_NATOMS function generic multicolvar vatom clusters adjmat volumes symfunc core gridtools matrixtools bias
21.037 Molecular Dynamics simulations of RBD/hACE2 complexes bio SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain Max Bonomi PRINT RMSD DISTANCE generic colvar
21.024 Property map collective variable as a useful tool for force field correction chemistry molecular mechanics Vojtech Spiwok PRINT PROPERTYMAP METAD TORSION BIASVALUE WHOLEMOLECULES generic colvar bias
21.021 ATLAS methods Machine Learning, Metadynamics Federico Giberti PRINT GROUP DUMPATOMS GYRATION METAD CONTACT_MATRIX COORDINATIONNUMBER UNITS TORSION MATHEVAL MATRIX_VECTOR_PRODUCT ONES MEAN WHOLEMOLECULES COORDINATION BIASVALUE DISTANCE function setup generic adjmat symfunc core matrixtools colvar bias
21.007 Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling bio metadynamics, machine learning, protein folding Vojtech Spiwok SUM POSITION FIT_TO_TEMPLATE COMBINE LESS_THAN MOLINFO ALPHARMSD MATHEVAL SECONDARY_STRUCTURE_RMSD WHOLEMOLECULES generic function colvar secondarystructure
20.011 Uremic toxin analysis bio metadynamics, uremic toxin, serum albumin Jim Pfaendtner SUM PRINT GROUP RESTART DISTANCES CENTER CUSTOM COORDINATION WHOLEMOLECULES DISTANCE function generic multicolvar vatom core colvar setup
20.006 Class B GPCR activation mechanism bio metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding Francesco Gervasio PRINT RMSD COMBINE LOWER_WALLS ENERGY UPPER_WALLS METAD MOLINFO CENTER MATHEVAL WHOLEMOLECULES DISTANCE function generic vatom colvar bias
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 SUM GROUP LESS_THAN ALPHABETA UPPER_WALLS TORSION CONSTANT CUSTOM PRINT ENDPLUMED WHOLEMOLECULES CS2BACKBONE ANTIBETARMSD COMBINE LOWER_WALLS FLUSH MOLINFO SECONDARY_STRUCTURE_RMSD PBMETAD BIASVALUE function generic multicolvar secondarystructure core isdb colvar bias
20.000 Muscarinic M2 receptor-ligand funnel metadynamics bio multiple walker metadynamics, well-tempered metadynamics, funnel metadynamics, MC-HLDA, GPCR, receptor, Adiabatic Bias MD Riccardo Capelli PRINT COMBINE LOWER_WALLS REWEIGHT_METAD METAD READ HISTOGRAM CONVERT_TO_FES COM MATHEVAL DUMPGRID ENDPLUMED UPPER_WALLS DISTANCE ABMD function generic vatom gridtools colvar bias
19.078 Iterative unbiasing of quasi-equilibrium sampling methods metadynamics, reweighting Federico Giberti PRINT GROUP DUMPATOMS METAD REWEIGHT_BIAS CONTACT_MATRIX COORDINATIONNUMBER UNITS ONES MATHEVAL MATRIX_VECTOR_PRODUCT COLLECT_FRAMES MEAN BIASVALUE DISTANCE function setup generic adjmat symfunc landmarks core matrixtools colvar bias
19.072 SINE hairpin MD+NMR bio metadynamics, RNA, NMR Giovanni Bussi PRINT INCLUDE FLUSH METAD TORSION MOLINFO COM MATHEVAL MAXENT SORT COORDINATION WHOLEMOLECULES DISTANCE function generic vatom colvar bias
19.071 Time-independent free energies from metadynamics via Mean Force Integration methods metadynamics, mean force integration, MFI, thermodynamic integration Matteo Salvalaglio PRINT COMMITTOR REWEIGHT_METAD METAD READ REWEIGHT_BIAS TORSION CONVERT_TO_FES MATHEVAL DUMPGRID EXTERNAL BIASVALUE DISTANCE HISTOGRAM function generic gridtools colvar bias
19.070 Unexpected Dynamics in the UUCG RNA Tetraloop bio well-tempered metadynamics, RNA, UUCG, maximum entropy Sandro Bottaro PRINT RMSD METAD TORSION MOLINFO ERMSD WHOLEMOLECULES DISTANCE generic colvar bias
19.062 Elucidating molecular design principles for charge-alternating peptides bio peptide folding, metadynamics, well-tempered ensemble, parallel tempering Jim Pfaendtner PRINT ENERGY GYRATION METAD WHOLEMOLECULES generic colvar bias
19.061 Diffusion in porous materials materials metadynamics, porous materials, diffusion Kim E. Jelfs PRINT GROUP LOWER_WALLS METAD RESTART CENTER COM UPPER_WALLS DISTANCE generic vatom bias core colvar setup
19.050 Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes chemistry metadynamics, membranes, Willard Chandler surface Gareth Tribello PRINT COMBINE READ REWEIGHT_BIAS METAD RESTART CONVERT_TO_FES DUMPGRID DISTANCE_FROM_CONTOUR UPPER_WALLS HISTOGRAM function setup generic contour gridtools bias
19.044 Multithermal-multibaric simulations using VES methods ves, Wang Landau, multicanonical, water, density anomaly Pablo Piaggi VES_LINEAR_EXPANSION REWEIGHT_TEMP_PRESS OPT_DUMMY HISTOGRAM VOLUME OPT_AVERAGED_SGD ENERGY ACCUMULATE AVERAGE CONVERT_TO_FES CUSTOM BF_LEGENDRE PRINT TD_MULTITHERMAL_MULTIBARIC REWEIGHT_BIAS DUMPGRID COMBINE READ RESTART function setup generic ves gridtools colvar bias
19.035 Dimerization of GPCRs from coarse-grained umbrella sampling bio Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization Davide Provasi PRINT GROUP RESTRAINT TORSION COM DISTANCE generic vatom core colvar bias
19.026 Ice Nucleation on Cholesterol Crystals materials forward flux sampling, crystal nucleation, water, ice, organic crystals Gabriele Cesare Sosso COMMITTOR FLUSH Q6 CONTACT_MATRIX DFSCLUSTERING LOCAL_Q6 ENDPLUMED CLUSTER_WITHSURFACE CLUSTER_NATOMS OUTPUT_CLUSTER MFILTER_MORE generic multicolvar adjmat clusters symfunc
19.024 PT-MetaD-WTE methods metadynamics, WTE, trp cage, PT Jim Pfaendtner GROUP ENERGY METAD EXTERNAL COORDINATION colvar bias core
19.015 Ibuprofen conformational dynamics and thermodynamics surface materials Ibuprofen, crystal, surface, solvents, conformers, metadynamics Matteo Salvalaglio PRINT LOWER_WALLS COMMITTOR METAD TORSION CENTER UPPER_WALLS DISTANCE generic vatom colvar bias
19.010 Multi-domain protein dynamics bio metainference, NMR, protein dynamics Carlo Camilloni SUM GROUP ALPHABETA CENTER DIHCOR UPPER_WALLS DISTANCE DHENERGY METAINFERENCE TORSION CONSTANT CUSTOM ENSEMBLE PRINT DIHEDRAL_CORRELATION ENDPLUMED WHOLEMOLECULES STATS RDC COMBINE RESTRAINT MOLINFO PBMETAD function generic multicolvar vatom core isdb colvar bias
19.006 Flying Gaussian proof methods flying Gaussians, alanine dipeptide Vojtech Spiwok PRINT METAD TORSION generic colvar bias
19.004 MI Ubiquitin bio metainference, NMR Max Bonomi RDC PRINT METAINFERENCE GROUP MOLINFO WHOLEMOLECULES CS2BACKBONE isdb generic core
19.002 EMMI STRA6 bio metainference, cryo-EM Max Bonomi PRINT GROUP MOLINFO BIASVALUE EMMI isdb generic bias core
19.000 VesDeltaF methods VES, convergence, suboptimal CVs Michele Invernizzi PRINT POSITION ENERGY METAD RESTART UNITS TORSION LOAD VES_DELTA_F ENDPLUMED setup generic ves colvar bias
24.036 Leveraging cryptic ligand envelopes through enhanced molecular simulations bio HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope Francesco Colizzi CONVERT_TO_FES DUMPGRID DISTANCE WHOLEMOLECULES GROUP ANGLE PRINT TORSION HISTOGRAM COORDINATION generic gridtools core colvar
24.011 Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble methods committor, machine learning Peilin Kang WHOLEMOLECULES PRINT UNITS UPPER_WALLS COORDINATION CELL GROUP MATHEVAL ENERGY DISTANCE TORSION LOWER_WALLS INCLUDE BIASVALUE ENDPLUMED MOLINFO CUSTOM LOAD RMSD POSITION core function bias generic colvar setup
24.003 Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations chemistry steered molecular dynamics, foldamers, peptoids, bio-inspired Kaylyn Torkelson WHOLEMOLECULES DISTANCE PRINT TORSION GYRATION COM ALPHABETA COORDINATION MOVINGRESTRAINT INCLUDE vatom bias generic colvar multicolvar
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 BIASVALUE MOLINFO GROUP WHOLEMOLECULES DISTANCE PRINT EMMIVOX WRAPAROUND UPPER_WALLS INCLUDE isdb colvar bias generic 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 BIASVALUE CENTER MOLINFO GROUP DISTANCE SAXS STATS PRINT ENSEMBLE RMSD WRAPAROUND UPPER_WALLS colvar isdb function vatom generic core bias
23.023 Rational design of novel biomimetic sequence-defined polymers for mineralization applications methods metadynamics, surface binding, biomimetic mineralization Kaylyn Torkelson DISTANCE PRINT GYRATION UPPER_WALLS COM COORDINATION PBMETAD generic vatom colvar bias
23.006 Transcription factor unbinding bio metadynamics, DNA, conformational changes Malin Lüking MOLINFO LESS_THAN DISTANCE ANGLE SECONDARY_STRUCTURE_RMSD PRINT METAD CONTACTMAP COM SUM ALPHARMSD DUMPFORCES vatom function secondarystructure bias generic colvar
23.002 Critical comparison of general-purpose collective variables for crystal nucleation methods metadynamics, umbrella sampling, commitor, entropy, PIV Julien Lam CUSTOM Q6 PRINT ENERGY PAIRENTROPY FUNCPATHMSD METAD VOLUME UNITS LOCAL_AVERAGE Q4 PIV UPPER_WALLS RESTRAINT piv symfunc gridtools function bias generic colvar setup
22.039 Driving and characterizing nucleation of urea and glycine polymorphs in water bio metadynamics, nucleation, amino acids, polymorphism Eric Beyerle PRINT MATRIX_VECTOR_PRODUCT MEAN GROUP COMBINE MATHEVAL CONTACT_MATRIX PAIRENTROPY METAD Q4 SUM CENTER Q6 MORE_THAN SPHERICAL_HARMONIC COORDINATIONNUMBER ONES INCLUDE CUSTOM LOAD vatom matrixtools gridtools symfunc adjmat function bias generic core setup
22.030 Mixing physics across temperatures with generative artificial intelligence methods REMD, Generative AI, DDPM Yihang Wang PRINT TORSION WHOLEMOLECULES generic colvar
22.023 Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy bio CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble Faidon Brotzakis BIASVALUE MOLINFO WHOLEMOLECULES GROUP PRINT TORSION COORDINATION EMMI RESTART COM RMSD UPPER_WALLS PBMETAD vatom isdb colvar bias generic core setup
22.017 Water regulates the residence time of Benzamidine in Trypsin bio ligand binding, water, opes, benzamidine trypsin, unbinding rates, machine learning, Deep-LDA, Deep-TICA Narjes Ansari CENTER GROUP WHOLEMOLECULES MATHEVAL DISTANCE CUSTOM COMMITTOR PRINT UPPER_WALLS FIXEDATOM LOWER_WALLS RMSD OPES_METAD COORDINATION FIT_TO_TEMPLATE PYTORCH_MODEL opes colvar function pytorch vatom generic core bias
22.012 Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT bio contact maps, protein-protein interactions Isabell-Louise Grothaus CENTER CONTACTMAP PRINT DISTANCE generic colvar vatom
22.011 Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck methods metadynamics, membrane permeation, protein folding Shams Mehdi WHOLEMOLECULES PRINT UPPER_WALLS MEAN XANGLES COMBINE MATHEVAL METAD YANGLES COM SUM DISTANCE TORSION LOWER_WALLS ZANGLES MOLINFO CUSTOM CONSTANT ALPHABETA function vatom generic colvar bias multicolvar
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 PRINT UNITS OPT_AVERAGED_SGD UPPER_WALLS COORDINATION BF_GAUSSIANS TD_UNIFORM ENERGY TD_WELLTEMPERED METAD BF_CUBIC_B_SPLINES BF_WAVELETS BF_CHEBYSHEV DISTANCE VES_OUTPUT_BASISFUNCTIONS FLUSH OPT_ADAM INCLUDE VES_LINEAR_EXPANSION POSITION BF_LEGENDRE ves bias generic colvar setup
21.051 Automatic learning of hydrogen-bond fixes in an AMBER RNA force field methods force field, RNA Giovanni Bussi BIASVALUE MOLINFO COMBINE WHOLEMOLECULES PRINT ERMSD METAD COORDINATION generic function colvar bias
21.039 Deep learning the slow modes for rare events sampling methods collective variables, machine learning, slow modes, deep-tica, opes Luigi Bonati WHOLEMOLECULES PRINT UNITS MATRIX_VECTOR_PRODUCT DISTANCE_MATRIX ECV_MULTITHERMAL ENVIRONMENTSIMILARITY PYTORCH_MODEL MEAN GROUP COMBINE CONTACT_MATRIX ENERGY VOLUME SUM DISTANCE Q6 TORSION MORE_THAN SPHERICAL_HARMONIC OPES_METAD ONES FLUSH ENDPLUMED OPES_EXPANDED MOLINFO INCLUDE CUSTOM LOAD CONTACTMAP RMSD opes envsim matrixtools symfunc colvar adjmat function pytorch generic core setup
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 ENDPLUMED PRINT TORSION METAD RANDOM_EXCHANGES PBMETAD INCLUDE generic colvar bias
21.025 Computational and biochemical analysis of type IV pilus dynamics and stability bio molecular dynamics, calcium binding, Type IV pilus Yasaman Karami UPPER_WALLS PRINT LOWER_WALLS DISTANCE generic colvar bias
21.020 Reweighted Jarzynski sampling methods free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions Kristof Bal CONVERT_TO_FES DUMPGRID PRINT UNITS MATRIX_VECTOR_PRODUCT OPT_AVERAGED_SGD UPPER_WALLS MEAN GROUP COMBINE CONTACT_MATRIX METAD TD_WELLTEMPERED ANN SUM RESTRAINT REWEIGHT_METAD BF_CHEBYSHEV DISTANCE MORE_THAN REWEIGHT_BIAS COORDINATIONNUMBER HISTOGRAM OPES_METAD ONES MOVINGRESTRAINT FLUSH BIASVALUE CUSTOM LOAD VES_LINEAR_EXPANSION CONSTANT ves annfunc opes matrixtools gridtools symfunc colvar function adjmat bias generic core setup
21.018 Localized Volume-based Metadynamics bio LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification Riccardo Capelli CONVERT_TO_FES DUMPGRID WHOLEMOLECULES PRINT COORDINATION UPPER_WALLS READ GROUP MATHEVAL METAD FIXEDATOM COM REWEIGHT_METAD DISTANCE HISTOGRAM FLUSH ENDPLUMED RMSD POSITION vatom gridtools colvar function bias generic core
20.034 Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations bio RNA, SARS-CoV-2, partial tempering Sandro Bottaro CENTER MOLINFO DISTANCE ABMD PRINT TORSION ERMSD RESTART vatom bias generic colvar setup
20.026 Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor bio Metadynamics, Umbrella sampling Brandon Peters CONVERT_TO_FES DUMPGRID WHOLEMOLECULES COMBINE CUSTOM CONSTANT PRINT MULTI_RMSD METAD RESTRAINT HISTOGRAM CONCATENATE RMSD_VECTOR POSITION REWEIGHT_METAD gridtools function bias valtools generic colvar
20.017 FISST methods FISST, force, peptide, sampling, tempering Glen Hocky BIASVALUE GROUP DISTANCE MATHEVAL PRINT ENERGY GYRATION FISST UNITS RESTRAINT fisst colvar function bias generic core setup
20.012 Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies bio metadynamics, well-tempered ensemble, ligand binding, binding affinity calculations, novel COLVAR, funnel restraints, Hamiltonian replica-exchange, PathCV, COMetPath, SWISH Francesco Gervasio BIASVALUE MOLINFO FUNCPATHGENERAL GROUP WHOLEMOLECULES LOAD DISTANCE MATHEVAL CONSTANT PRINT METAD CONTACTMAP COM LOWER_WALLS UPPER_WALLS PROJECTION_ON_AXIS INCLUDE vatom colvar function bias generic core setup
20.007 Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics bio metadynamics, loop movement, artificial intelligence Pratyush Tiwary MOLINFO WHOLEMOLECULES DISTANCE COMBINE PRINT TORSION METAD RESTART RMSD UPPER_WALLS function bias generic colvar setup
20.002 Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study bio Metadynamics, path CVs Riccardo Ocello MOLINFO WHOLEMOLECULES GROUP PRINT METAD PATHMSD RESTART UPPER_WALLS colvar bias generic core setup
19.068 Rethinking Metadynamics methods metadynamics, opes, convergence Michele Invernizzi ENDPLUMED EXTERNAL PRINT TORSION METAD UNITS OPES_METAD POSITION opes bias generic colvar setup
19.058 Constrained MD for maintaining a cavity in a calculation chemistry constrained MD, porous molecules, porosity, cavity Kim Jelfs CUSTOM DISTANCE ANGLE PRINT INPLANEDISTANCES RESTART COM SUM DISTANCES MOVINGRESTRAINT FLUSH function vatom generic colvar setup bias multicolvar
19.042 Harmonic Linear Discriminant Analysis (HLDA) methods metadynamics, chemistry, HLDA GiovanniMaria Piccini COMBINE DISTANCE PRINT ENERGY METAD UNITS UPPER_WALLS FLUSH function bias generic colvar setup
19.039 Funnel Metadynamics bio funnel-metadynamics, absolute binding free energy, ligand-receptor complexes Vittorio Limongelli WHOLEMOLECULES FUNNEL_PS DISTANCE PRINT METAD FUNNEL COM RMSD LOWER_WALLS UPPER_WALLS funnel vatom generic colvar bias
19.036 Thermodynamics and kinetics of G protein-coupled receptor activation bio metadynamics, allostery, receptor conformation, GPCR, pharmacology Davide Provasi ENDPLUMED WHOLEMOLECULES DISTANCE PRINT FUNCPATHMSD METAD CONTACTMAP COM RMSD function vatom generic colvar bias
19.013 RNA FF FITTING methods force field, RNA Giovanni Bussi BIASVALUE MOLINFO MATHEVAL PUCKERING CONSTANT TORSION INCLUDE generic function colvar bias
19.005 Cmyc small molecule interaction bio metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP Gabriella Heller CENTER MOLINFO METAINFERENCE GROUP WHOLEMOLECULES DISTANCE PRINT GYRATION ALPHABETA COORDINATION CS2BACKBONE PBMETAD INCLUDE colvar isdb vatom generic core bias multicolvar
25.003 Surrogate Model CV methods Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding Sompriya Chatterjee DISTANCE OPES_METAD MOLINFO ENDPLUMED PYTORCH_MODEL GROUP COMBINE TORSION PRINT CUSTOM MATHEVAL COMMITTOR WHOLEMOLECULES ENERGY core colvar pytorch generic function opes
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 DISTANCE OPES_METAD PRINT UPPER_WALLS COORDINATION ENERGY bias colvar opes generic
24.004 Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables materials metadynamics, nucleation, machine learning Ziyue Zou GROUP METAD PRINT RESTART LOAD INCLUDE setup bias core generic
24.000 Ammonia Decomposition on Non-stoichiometric Lithium Imide chemistry ammonia decomposition, non-stoichiometric lithium imide, machine learning interatomic potentials, enhanced sampling, heterogeneous catalysis Francesco Mambretti DISTANCE OPES_METAD SUM COORDINATIONNUMBER FLUSH CONTACT_MATRIX GROUP FIXEDATOM ZDISTANCES PRINT CUSTOM UPPER_WALLS ONES MEAN UNITS MATRIX_VECTOR_PRODUCT setup multicolvar colvar core symfunc matrixtools adjmat generic vatom bias function opes
23.034 Urea nucleation in water: do long-range forces matter? materials LMF theory, Metadynamics, Nucleation Ziyue Zou SUM COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT GROUP CONTACT_MATRIX MORE_THAN METAD CENTER PRINT CUSTOM ONES MEAN LOAD INCLUDE setup core generic symfunc adjmat matrixtools vatom bias function
23.032 Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics bio metadynamics, tSNE, neural network, machine learning, trp-cage, folding Vojtech Spiwok ALPHARMSD MOLINFO SUM FIT_TO_TEMPLATE LESS_THAN COMBINE METAD PRINT SECONDARY_STRUCTURE_RMSD WHOLEMOLECULES ANN POSITION colvar annfunc secondarystructure generic bias function
23.026 Machine Learning Nucleation Collective Variables with Graph Neural Networks chemistry Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks Florian Dietrich LOWER_WALLS COORDINATIONNUMBER GROUP COMBINE METAD PRINT Q6 LOCAL_Q6 MOVINGRESTRAINT MFILTER_MORE multicolvar core symfunc generic bias function
23.012 JAK2 2D meta-eABF PMF with statistical analysis bio 2D meta-eABF, path CV, PMF Istvan Kolossvary LOWER_WALLS PATHMSD METAD PRINT CUSTOM BIASVALUE UPPER_WALLS DRR FLUSH colvar drr generic bias function
23.011 OneOPES, a combined enhanced sampling method to rule them all bio OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding Valerio Rizzi DISTANCE MOLINFO OPES_METAD_EXPLORE ENDPLUMED METAD TORSION PRINT OPES_EXPANDED ECV_MULTITHERMAL ENERGY bias colvar opes generic
23.010 An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands bio GPCR, binding free energy, free energy surface Timothy Clark DISTANCE LOWER_WALLS CONSTANT METAD PRINT UPPER_WALLS MATHEVAL BIASVALUE WHOLEMOLECULES function bias colvar generic
23.004 Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point chemistry water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential Pablo Piaggi SUM LOWER_WALLS HISTOGRAM GROUP MORE_THAN PRINT ECV_UMBRELLAS_LINE CUSTOM OPES_EXPANDED UPPER_WALLS ONES RESTART DISTANCE_MATRIX DUMPGRID ENVIRONMENTSIMILARITY MATRIX_VECTOR_PRODUCT setup core matrixtools adjmat gridtools generic envsim bias function opes
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 MOLINFO GYRATION TORSION PBMETAD WHOLEMOLECULES bias colvar 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 METAD PRINT CUSTOM BIASVALUE DRR FLUSH colvar drr generic bias function
22.024 Conformational Entropy as a Potential Liability of Computationally Designed Antibodies bio metadynamics, conformational entropy, antibody, nanobody Thomas Löhr ALPHABETA ALPHARMSD MOLINFO SUM ANTIBETARMSD CONSTANT LESS_THAN COMBINE TORSION SECONDARY_STRUCTURE_RMSD PRINT CUSTOM COM RESTART PBMETAD WHOLEMOLECULES setup multicolvar colvar secondarystructure generic vatom bias function
22.018 Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations bio ligand binding, docking, EMMI, LAT1 Max Bonomi MOLINFO GROUP PRINT BIASVALUE EMMIVOX LOAD WHOLEMOLECULES setup core isdb generic bias
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 DISTANCE MOLINFO EMMI GROUP COM PRINT UPPER_WALLS BIASVALUE RESTART WHOLEMOLECULES setup core colvar isdb generic vatom bias
21.036 Modelling the structure and interactions of intrinsically disordered peptides with multiple-replica, metadynamics-based sampling methods and force-field combinations bio Bias Exchange Metadynamics, PTWTE-metaD Matteo Salvalaglio ANTIBETARMSD MOLINFO LOWER_WALLS PRINT COORDINATION DIHCOR GYRATION LESS_THAN METAD UPPER_WALLS WHOLEMOLECULES RANDOM_EXCHANGES GROUP SECONDARY_STRUCTURE_RMSD DIHEDRAL_CORRELATION PARABETARMSD ENERGY ALPHARMSD SUM LOWEST multicolvar colvar core secondarystructure generic bias function
21.017 All-atom simulations of the Vav1 AD construct bio metadynamics, parallel-bias, well-tempered Simone Orioli ALPHABETA ALPHARMSD MOLINFO SUM CONSTANT GROUP LESS_THAN REWEIGHT_BIAS COMBINE METAD TORSION SECONDARY_STRUCTURE_RMSD PRINT CUSTOM RESTART PBMETAD WHOLEMOLECULES CONTACTMAP setup multicolvar core colvar secondarystructure generic bias function
21.015 Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin bio metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module Gaston Courtade RESTRAINT REWEIGHT_BIAS METAD CENTER PRINT MATHEVAL RESTART WHOLEMOLECULES COORDINATION POSITION setup colvar generic vatom bias function
21.013 Role of vibrational excitation in heterogeneous catalysis chemistry catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption Kristof Bal DISTANCE LOWER_WALLS COORD_ANGLES CONTACT_MATRIX OPT_AVERAGED_SGD COMBINE PRINT VES_LINEAR_EXPANSION COORDINATION EXTERNAL DISTANCES TD_GRID METAD CUSTOM UPPER_WALLS UWALLS FLUSH MATRIX_VECTOR_PRODUCT RESTRAINT HISTOGRAM COORDINATIONNUMBER GROUP BF_CHEBYSHEV MEAN LOAD UNITS ANGLES REWEIGHT_BIAS REWEIGHT_METAD CONVERT_TO_FES ONES DUMPGRID setup ves multicolvar colvar core symfunc matrixtools adjmat gridtools generic bias function
20.024 Gaussian Mixture Based Enhanced Sampling (GAMBES) methods enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias Jayashrita Debnath DISTANCE DISTANCES LOWER_WALLS GROUP COMBINE TORSION PRINT ENERGY UPPER_WALLS LOAD UNITS setup multicolvar colvar core generic bias function
20.023 metadynminer and metadynminer3d methods metadynamics, visualization, R Vojtech Spiwok METAD TORSION PRINT bias 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 MOLINFO PRINT STATS WHOLEMOLECULES COORDINATION bias function colvar generic
19.069 Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen materials ibuprofen, crystal, solvent, surface Matteo Salvalaglio DISTANCE ENDPLUMED GROUP CENTER PRINT INCLUDE vatom colvar core generic
19.066 Finding ligand unbinding reaction pathways methods maze, ligand unbinding Jakub Rydzewski MAZE_OPTIMIZER_BIAS PRINT UNITS MAZE_LOSS POSITION MAZE_SIMULATED_ANNEALING maze setup colvar generic
19.057 SAXS ensembles using Martini-Beads multi-scale SAXS methods metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics Cristina Paissoni ALPHABETA MOLINFO ENDPLUMED ANGLE GROUP COMBINE CENTER PRINT MATHEVAL BIASVALUE SAXS ENSEMBLE STATS PBMETAD WHOLEMOLECULES COORDINATION INCLUDE multicolvar colvar core isdb generic vatom bias function
19.021 Coarse-Grained Directed Simulation methods experiment directed simulation, coarse-grain, bias Glen Hocky DISTANCE RESTRAINT COMBINE TORSION PRINT EDS colvar generic eds bias function
19.003 EMMI ClpP bio metainference, cryo-EM Max Bonomi MOLINFO EMMI GROUP PRINT BIASVALUE bias core isdb generic
25.001 RNA G-quadruplex folding with ST-metaD protocol bio RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD Pavlína Pokorná WHOLEMOLECULES MOLINFO METAD COMBINE ERMSD function generic bias colvar
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 UPPER_WALLS LOWER_WALLS DISTANCE GROUP CUSTOM PRINT COMMITTOR OPES_METAD COORDINATION UNITS RESTART function colvar bias core setup generic opes
24.029 Combination of OPES and OPES-Explore methods OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin Dhiman Ray LOWER_WALLS BIASVALUE RMSD OPES_METAD_EXPLORE ENERGY FIXEDATOM PYTORCH_MODEL MOLINFO UPPER_WALLS CENTER PRINT COMBINE COORDINATION UNITS CONTACTMAP WHOLEMOLECULES DISTANCE FLUSH GROUP CUSTOM OPES_METAD POSITION METAD FIT_TO_TEMPLATE INCLUDE MATHEVAL ENDPLUMED pytorch function vatom colvar bias core setup generic opes
24.028 All-atom simulations of RNA-membrane interactions bio metadynamics, membrane, RNA Giovanni Bussi WHOLEMOLECULES MOLINFO UPPER_WALLS CENTER DISTANCE POSITION GROUP METAD PRINT COMBINE SORT LOWEST MATHEVAL GHOST DISTANCES function vatom colvar multicolvar bias core generic
24.020 Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics bio LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning Ziyue Zou, Dedi Wang, Pratyush Tiwary TORSION METAD GROUP PRINT COMMITTOR LOAD colvar bias core setup generic
24.019 Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning bio OPES, machine learning, protein folding, adaptive sampling Mingyuan Zhang WHOLEMOLECULES TORSION MOLINFO LESS_THAN GYRATION DISTANCE SUM SECONDARY_STRUCTURE_RMSD CUSTOM PRINT OPES_METAD COMBINE ALPHARMSD COORDINATION secondarystructure colvar generic function opes
24.010 Oxytocin metadynamics simulation bio metadynamics, oxytocin, peptide Jan Beránek WHOLEMOLECULES TORSION FLUSH METAD PRINT RESTART setup generic bias colvar
23.046 Lasso Peptides - HLDA CV bio metadynamics, protein folding, HLDA, harmonic Gabriel da Hora WHOLEMOLECULES DISTANCE METAD PRINT COMBINE UNITS colvar generic bias setup function
23.039 Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation chemistry metadynamics, ligand dissociation Eric Beyerle UPPER_WALLS MOLINFO CENTER DISTANCE RESTRAINT METAD PRINT COMBINE DUMPMASSCHARGE FIXEDATOM vatom colvar generic bias function
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 LOWER_WALLS BIASVALUE OPES_METAD_EXPLORE ENERGY WRAPAROUND TORSION MOLINFO UPPER_WALLS CENTER PRINT COORDINATION UNITS WHOLEMOLECULES COM DISTANCE FLUSH GROUP CUSTOM COMMITTOR OPES_METAD POSITION FIT_TO_TEMPLATE MATHEVAL ENDPLUMED function vatom colvar bias core setup generic opes
23.020 FEP simulations of ATOX1 homodimer chemistry parallel bias metadynamics, FEP, free-energy of metal ion dissociation Adriana Pietropaolo WHOLEMOLECULES DISTANCE PBMETAD BIASVALUE CONSTANT PRINT ANGLE MATHEVAL function generic bias colvar
23.013 Path meta-eABF simulation of large scale conformational change in STING protein methods meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint Istvan Kolossvary PATHMSD UPPER_WALLS LOWER_WALLS TIME METAD FLUSH CUSTOM BIASVALUE PRINT DRR UNITS drr colvar generic bias setup function
22.033 Reciprocal barrier restraint. Application to PROTAC passive permeability prediction methods PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR Istvan Kolossvary COM DISTANCE FLUSH METAD CUSTOM BIASVALUE PRINT DRR UNITS drr vatom colvar generic bias setup function
22.031 Rare Event Kinetics from Adaptive Bias Enhanced Sampling methods OPES Flooding, Kinetics, Rate, OPES, Machine Learning Dhiman Ray BIASVALUE RMSD ENERGY PYTORCH_MODEL TORSION MOLINFO PRINT COMBINE UNITS CONTACTMAP WHOLEMOLECULES DISTANCE GROUP CUSTOM CONSTANT COMMITTOR OPES_METAD POSITION INCLUDE ENDPLUMED pytorch colvar generic bias core setup function opes
22.022 Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir bio RMSD, protein-ligand interactions Isabell Grothaus PRINT RMSD generic colvar
22.019 Exploring aspartic protease inhibitor binding to design selective antimalarials bio ligand binding, loop opening, path CV, funnel metadynamics, drug development Raitis Bobrovs WHOLEMOLECULES PATHMSD UPPER_WALLS COM LOWER_WALLS DISTANCE METAD PRINT FUNNEL_PS FUNNEL vatom colvar bias generic funnel
22.014 Quasi Liquid Layer Order Parameters materials Quasi-Liquid Layer, Steinhardt Order Parameter, Entropy Fingerprint Jihong Shi Q6 DUMPMULTICOLVAR LOCAL_AVERAGE Q4 Q3 HISTOGRAM LOCAL_Q3 LOCAL_Q4 LOCAL_Q6 PAIRENTROPIES UNITS DUMPGRID ENDPLUMED LOAD symfunc multicolvar setup generic gridtools
21.049 Multiple-path-metadynamics and PathMaps methods path-CV, metadynamics, multiple-walker, multiple paths, pathmap Alberto Pérez-de-Alba-Ortíz TORSION UPPER_WALLS RESTRAINT LOWER_WALLS MOVINGRESTRAINT METAD CUSTOM PRINT CONSTANT COMBINE UNITS ENSEMBLE LOAD function colvar bias setup generic
21.029 Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs bio metadynamics, small peptide, machine learning Pratyush Tiwary EXTERNAL TORSION MOLINFO FLUSH PRINT RESTART ENERGY setup generic bias 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 PRINT generic
21.009 Nucleation rates from small scale atomistic simulations and transition state theory materials kinetics, free energy barriers, nucleation, droplets, metadynamics Kristof Bal MEAN MORE_THAN HISTOGRAM LOAD UPPER_WALLS PRINT ONES UNITS MATRIX_VECTOR_PRODUCT SUM FLUSH GROUP COMMITTOR DUMPGRID REWEIGHT_METAD CONVERT_TO_FES MOVINGRESTRAINT CONTACT_MATRIX METAD COORDINATIONNUMBER function adjmat symfunc matrixtools bias core setup generic gridtools
20.027 Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery bio SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery Khaled Abdel-Maksoud TORSION PRINT METAD DISTANCE generic bias colvar
20.025 The role of water in host-guest interaction bio ligand binding, water, opes, SAMPL5 Valerio Rizzi WHOLEMOLECULES UPPER_WALLS CENTER DISTANCE GROUP PRINT FIT_TO_TEMPLATE OPES_METAD COORDINATION ANGLE ENERGY MATHEVAL ENDPLUMED FIXEDATOM PYTORCH_MODEL function pytorch vatom colvar bias core generic opes
20.020 Parallel Bias Metadynamics methods pbmetad, trp-cage, folding Max Bonomi WHOLEMOLECULES TORSION MOLINFO GYRATION DIHCOR PBMETAD SUM CUSTOM PRINT CONSTANT ALPHABETA COMBINE COORDINATION DIHEDRAL_CORRELATION INCLUDE colvar multicolvar generic bias function
20.015 Rational design of ASCT2 inhibitors using an integrated experimental-computational approach bio ASCT2 transporter, small-molecules, cryo-EM, metainference Max Bonomi WHOLEMOLECULES DUMPATOMS MOLINFO EMMIVOX GROUP BIASVALUE PRINT LOAD isdb bias core setup generic
20.008 Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol chemistry proton trasfer, metadynamics Kevin Rossi DISTANCE SUM METAD CUSTOM PRINT COORDINATION UNITS DISTANCES function colvar multicolvar bias setup 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 LOWER_WALLS HISTOGRAM READ MOLINFO UPPER_WALLS PRINT COMBINE ABMD CONTACTMAP WHOLEMOLECULES COM DISTANCE FLUSH DUMPGRID REWEIGHT_METAD CONVERT_TO_FES METAD ENDPLUMED FUNCPATHMSD vatom colvar generic bias function gridtools
19.083 Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis chemistry metadynamics, chemical reactions, reaction discovery Valerio Rizzi MEAN UPPER_WALLS DISTANCE SUM FLUSH CONTACT_MATRIX GROUP CUSTOM METAD PRINT ONES COMBINE COORDINATIONNUMBER UNITS RESTART ENDPLUMED MATRIX_VECTOR_PRODUCT DISTANCES function adjmat symfunc colvar matrixtools multicolvar bias core setup generic
19.082 Ammonia Borane Dehydrogenation chemistry metadynamics, reaction discovery, hydrogen production, chemistry Valerio Rizzi EXTERNAL MEAN SUM FLUSH CONTACT_MATRIX GROUP CUSTOM METAD PRINT ONES COMBINE COORDINATIONNUMBER UNITS RESTART ENDPLUMED MATRIX_VECTOR_PRODUCT function adjmat symfunc matrixtools bias core setup generic
19.076 Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones bio molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics Salvatore Assenza GYRATION MOVINGRESTRAINT PRINT UNITS ENDPLUMED setup generic bias colvar
19.065 Molecular Enhanced Sampling with Autoencoders methods enhanced sampling, collective variables, deep learning Wei Chen RESTRAINT COM POSITION COMBINE ANN vatom colvar annfunc bias function
19.063 Protein-ligand binding through metadynamics with path CVs bio metadynamics, path CVs, ligand binding Mattia Bernetti WHOLEMOLECULES PATHMSD UPPER_WALLS LOWER_WALLS METAD PRINT generic bias 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 WHOLEMOLECULES TORSION MOLINFO COM UPPER_WALLS LOWER_WALLS DISTANCE GROUP METAD PRINT ALPHABETA FUNNEL RMSD COMBINE BRIDGE REWEIGHT_METAD DISTANCES function adjmat vatom colvar multicolvar bias core generic funnel
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 UPPER_WALLS LOWER_WALLS POSITION FLUSH GROUP METAD PRINT COORDINATION UNITS RESTART colvar bias core setup generic
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 METAD PRINT ENERGY generic vatom bias colvar
19.022 eABF simulation of NANMA (alanine dipeptide) methods eABF, DRR, alanine dipeptide Haochuan Chen TORSION PRINT DRR drr generic colvar
19.019 FA-MetaD-JCP-Wang-et-al bio Frequency adaptive metadynamics; peptide Kresten Lindorff-Larsen TORSION MOLINFO SUM FLUSH METAD CUSTOM PRINT CONSTANT ALPHABETA COMMITTOR COMBINE colvar multicolvar generic bias function
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 COM PARABETARMSD GROUP DISTANCE DUMPMASSCHARGE CENTER WHOLEMOLECULES EMMI SECONDARY_STRUCTURE_RMSD RMSD SUM LOWEST ALPHARMSD BIASVALUE UPPER_WALLS LESS_THAN MOLINFO COORDINATION PRINT PBMETAD DUMPATOMS core function bias secondarystructure colvar vatom generic isdb
24.032 DeepLNE++ methods PATHCV, OPES Thorben Fröhlking GROUP DISTANCE COMBINE COORDINATION ENERGY OPES_METAD LOAD TORSION PRINT CUSTOM function generic colvar core setup opes
24.024 Host-Guest binding free energies à la carte, an automated OneOPES protocol bio OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest Valerio Rizzi GROUP ENDPLUMED OPES_METAD_EXPLORE ECV_MULTITHERMAL DISTANCE COORDINATION ENERGY TORSION ANGLE CENTER FIT_TO_TEMPLATE MATHEVAL PRINT WHOLEMOLECULES LOWER_WALLS FIXEDATOM OPES_EXPANDED UPPER_WALLS core function bias colvar vatom generic opes
24.023 Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21. A Machine-Learning-Aided Enhanced Sampling Study bio RNA, miRNA, OneOPES, ligand binding, conformational changes Valerio Rizzi GROUP OPES_METAD_EXPLORE ECV_MULTITHERMAL DISTANCE COMBINE COORDINATION ENERGY RESTART TORSION PRINT OPES_EXPANDED CUSTOM function generic colvar core setup opes
24.017 Absolute Binding Free Energies with OneOPES methods protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy Francesco Gervasio COM GROUP CONTACTMAP PROJECTION_ON_AXIS WHOLEMOLECULES INCLUDE OPES_METAD_EXPLORE ENERGY METAD RMSD LOWER_WALLS OPES_EXPANDED RESTART MATHEVAL BIASVALUE UPPER_WALLS MOLINFO WRAPAROUND COORDINATION ECV_MULTITHERMAL TORSION PRINT CUSTOM CONSTANT core function bias colvar vatom generic setup opes
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 MOLINFO COORDINATION PYTORCH_MODEL METAD DRR FLUSH RMSD PRINT WHOLEMOLECULES LOWER_WALLS UPPER_WALLS bias drr colvar pytorch generic
24.013 Estimating Free Energy Surfaces and their Convergence from multiple, independent static and history-dependent biased molecular-dynamics simulations with Mean Force Integration methods Mean Force Integration, Convergence, FES, Umbrella Sampling Matteo Salvalaglio MOLINFO DISTANCE RESTRAINT ENERGY COORDINATIONNUMBER METAD TORSION RESTART FLUSH MATHEVAL PRINT BIASVALUE COMMITTOR function bias symfunc colvar generic setup
24.007 SWISH-X bio swish-x, SWISH-X, swish, expanded SWISH Alberto Borsatto INCLUDE MOLINFO ECV_MULTITHERMAL CONTACTMAP ENERGY PRINT WHOLEMOLECULES OPES_EXPANDED UPPER_WALLS generic colvar bias opes
24.005 Learning Markovian Dynamics with Spectral Maps methods spectral map, collective variables, machine learning Jakub Rydzewski DISTANCE UNITS PRINT BIASVALUE CUSTOM function bias colvar generic setup
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 DISTANCE COMBINE OPES_METAD UNITS FLUSH TORSION PRINT LOWER_WALLS COMMITTOR CUSTOM UPPER_WALLS function bias colvar generic setup opes
23.019 Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors bio binding pathway, binding energy, sketch-map, drug development Raitis Bobrovs COM DISTANCE PATHMSD COLLECT_FRAMES WHOLEMOLECULES PROJECT_POINTS SKETCHMAP_PROJECTION METAD PDB2CONSTANT TRANSPOSE SUM DISSIMILARITIES VSTACK LANDMARK_SELECT_FPS SKETCHMAP UPPER_WALLS VORONOI MORE_THAN EUCLIDEAN_DISTANCE PRINT CUSTOM CONSTANT refdist dimred matrixtools function valtools bias colvar vatom generic landmarks
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 GROUP DISTANCE CONTACTMAP CENTER WHOLEMOLECULES ENDPLUMED COMMITTOR INCLUDE ENERGY COMBINE ANGLE RMSD LOWER_WALLS OPES_METAD FIT_TO_TEMPLATE MATHEVAL UPPER_WALLS MOLINFO COORDINATION PYTORCH_MODEL PRINT FIXEDATOM CUSTOM core function bias colvar vatom pytorch generic opes
22.044 Colloid Crystallisation Analyses materials Q4, Q6, Pair Entropy, DFS Aaron Finney GROUP LOCAL_Q4 MFILTER_LESS COORDINATIONNUMBER COMBINE LOCAL_Q6 MFILTER_MORE Q6 Q4 CONTACT_MATRIX PRINT CLUSTER_NATOMS LOCAL_AVERAGE DFSCLUSTERING adjmat multicolvar function clusters symfunc generic core
22.042 Metadynamics of NSP10 and variants bio metadynamics, NSP10, crystal structure, variants Shozeb Haider TORSION PRINT METAD generic colvar bias
22.037 Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site chemistry metadynamics, DNA, abasic Mike Jones GROUP DISTANCE METAD DISTANCES CENTER PRINT MEAN multicolvar function bias generic colvar vatom core
22.025 Bubble nucleation rate predictions in a Lennard-Jones fluid materials free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation Kristof Bal GROUP RESTRAINT REWEIGHT_BIAS VOLUME ONES COMMITTOR MOVINGRESTRAINT MATRIX_VECTOR_PRODUCT DUMPGRID HISTOGRAM ANN CONTACT_MATRIX SUM COORDINATIONNUMBER LOAD FLUSH BIASVALUE UPPER_WALLS LESS_THAN CONVERT_TO_FES UNITS PRINT MEAN CUSTOM adjmat core gridtools matrixtools annfunc function bias symfunc colvar generic setup
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 GROUP INCLUDE MATRIX_VECTOR_PRODUCT ENVIRONMENTSIMILARITY MORE_THAN SUM DISTANCE_MATRIX MEAN OPES_EXPANDED ONES PRINT LOWER_WALLS ECV_UMBRELLAS_LINE CUSTOM UPPER_WALLS adjmat core matrixtools function bias envsim generic opes
22.015 Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome bio photodynamics, bacteriophytochrome, variationally enhanced sampling Jakub Rydzewski VES_LINEAR_EXPANSION BF_FOURIER OPT_AVERAGED_SGD PRINT TORSION TD_UNIFORM ves generic colvar
22.013 Ligand dissociation from PreQ1 riboswitch bio ligand, RNA, metadynamics, pRAVE Yihang Wang COM GROUP MOLINFO DISTANCE COMBINE COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT METAD SUM CONTACT_MATRIX RMSD PRINT WHOLEMOLECULES MEAN COMMITTOR CUSTOM ONES adjmat core matrixtools function bias symfunc colvar vatom generic
21.052 On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets materials Ibuprofen, unbinding, WTmetaD Matteo Salvalaglio GROUP ENDPLUMED DISTANCE COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT METAD CONTACT_MATRIX CENTER TORSION PRINT MEAN COMMITTOR ONES adjmat core matrixtools function bias symfunc colvar vatom generic
21.045 QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP) chemistry metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange Denis Maag GROUP DISTANCE COMBINE COORDINATION COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT METAD MEAN CONTACT_MATRIX ONES PRINT LOWER_WALLS UPPER_WALLS adjmat matrixtools function bias symfunc generic colvar core
21.042 Peptoid-mediated Au nanocrystal growth materials parallel-bias metadynamics, peptoid, Au Xin Qi COM MOLINFO DISTANCE GYRATION PRINT PBMETAD UPPER_WALLS generic colvar vatom bias
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 PBMETAD UNITS WHOLEMOLECULES core bias colvar generic setup
21.031 Photo-switchable sulfonulureas in KATP channel bio metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels Katarzyna Walczewska-Szewc COM DISTANCE METAD UNITS PRINT WHOLEMOLECULES LOWER_WALLS UPPER_WALLS bias colvar vatom generic setup
21.030 Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains bio parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure Jim Pfaendtner COM INCLUDE DISTANCE COMBINE COORDINATION ENERGY GYRATION METAD SUM ALPHABETA TORSION PRINT PBMETAD CUSTOM CONSTANT function multicolvar bias colvar vatom generic
21.022 Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly materials parallel bias metadynamics, adsorption, peptide Xin Qi COM MOLINFO DISTANCE ENERGY GYRATION PRINT PBMETAD LOWER_WALLS UPPER_WALLS generic colvar vatom bias
21.008 Multi-replica biased sampling for photoisomerization processes in conjugated polymers methods metadynamics, FEP, replica-exchange Adriana Pietropaolo MATHEVAL PBMETAD RESTART TORSION PRINT WHOLEMOLECULES BIASVALUE CONSTANT function bias colvar generic setup
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 MOLINFO COORDINATION COMBINE RESTRAINT PRINT WHOLEMOLECULES STATS generic colvar function bias
20.018 Free energy barriers from biased molecular dynamics simulations methods kinetics, free energy barriers, chemical reactions, nucleation, metadynamics Kristof Bal DISTANCE REWEIGHT_METAD REWEIGHT_BIAS CENTER LOCAL_AVERAGE VOLUME PAIRENTROPY COMBINE DUMPGRID ENERGY METAD HISTOGRAM CONTACT_MATRIX LOWER_WALLS COORDINATIONNUMBER LOAD Q6 FLUSH UPPER_WALLS DENSITY COORDINATION CONVERT_TO_FES UNITS PRINT SPRINT adjmat sprint gridtools function bias symfunc volumes colvar vatom generic setup
19.053 Capillary fluctuations with PLUMED methods nucleation, surface tension, capillary fluctuations Gareth Tribello GROUP ACCUMULATE MULTICOLVARDENS CENTER ONES MATRIX_VECTOR_PRODUCT DUMPGRID FCCUBIC_FUNC CONTACT_MATRIX DISTANCES FCCUBIC SUM CHARGE FOURIER_TRANSFORM MORE_THAN POSITION UNITS KDE MASS ARGS2VATOM FIND_CONTOUR_SURFACE CUSTOM adjmat fourier core gridtools matrixtools multicolvar function contour symfunc colvar vatom generic setup
19.047 Close Structure methods metadynamics, RMSD, path collective variables, property map Vojtech Spiwok PROPERTYMAP PRINT WHOLEMOLECULES METAD generic colvar bias
19.037 Scission free energy of organic dyes chemistry metadynamics, multiple walkers, matheval/lepton Paolo Raiteri DISTANCE METAD UNITS RESTART FLUSH MATHEVAL PRINT UPPER_WALLS function bias colvar generic setup
19.018 Excited state FEP/Metadynamics simulations chemistry metadynamics, FEP, excited states, conjugated polymers, torsional potential Adriana Pietropaolo MATHEVAL METAD TORSION PRINT WHOLEMOLECULES BIASVALUE CONSTANT generic function colvar bias
19.017 Ligand binding pathways exploration bio metadynamics, ligand binding Riccardo Capelli COM GROUP ENDPLUMED WRAPAROUND COORDINATION DUMPGRID METAD REWEIGHT_METAD POSITION HISTOGRAM CONVERT_TO_FES FLUSH FIT_TO_TEMPLATE MATHEVAL PRINT WHOLEMOLECULES READ UPPER_WALLS core gridtools function bias colvar vatom generic
24.025 Correlating Enzymatic Reactivity for Different Substrates using Transferable Data-Driven Collective Variables bio enzymatic reactivity, k_cat, transfer learning, data-driven CVs, catalysis, ligand-binding modes, water, alpha-amylase, sugar, classical MD, OPES, machine learning, Deep TDA CV, path CV Sudip Das COMBINE LOWER_WALLS COORDINATION LOWEST CONSTANT SUM RESTART PDB2CONSTANT OPES_METAD PATH FIXEDATOM GROUP DISTANCE CUSTOM TORSION WHOLEMOLECULES CENTER PYTORCH_MODEL UPPER_WALLS EUCLIDEAN_DISTANCE FIT_TO_TEMPLATE vatom generic refdist mapping opes core function colvar pytorch bias setup
24.012 Molecular simulations to investigate the impact of N6-methylation in RNA recognition bio metadynamics, alchemistry, RNA modification, RNA:protein interactions Giovanni Bussi COMBINE LOWER_WALLS BIASVALUE CENTER COORDINATION MOLINFO COM GHBFIX UPPER_WALLS DEBUG PRINT METAD GROUP DISTANCE vatom generic core function colvar bias
23.044 Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition materials metadynamics, interlocked molecules Luigi Leanza DUMPGRID CONVERT_TO_FES COORDINATION HISTOGRAM READ PRINT ENDPLUMED METAD GROUP COMMITTOR generic core colvar bias gridtools
23.040 Supramolecular capsules assembly dynamics chemistry Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics Riccardo Capelli METAD POSITION LESS_THAN CUSTOM BETWEEN WHOLEMOLECULES CENTER FLUSH UNITS PRINT DISTANCES COM SUM GROUP DISTANCE vatom generic multicolvar core colvar function bias setup
23.038 Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor bio protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics Timothy Clark WHOLEMOLECULES RMSD MATHEVAL MOLINFO PRINT METAD DISTANCE bias colvar function generic
23.036 Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? bio NaCl, nucleation, metadynamics Ruiyu Wang COMBINE METAD Q4 MORE_THAN VOLUME ONES MEAN COORDINATIONNUMBER CUSTOM MATRIX_VECTOR_PRODUCT CONTACT_MATRIX Q6 ENERGY SPHERICAL_HARMONIC MATHEVAL PRINT SUM GROUP generic core adjmat function colvar matrixtools bias symfunc
23.035 An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors bio G protein coupled receptor, peptide ligands, metadynamics, multiple-walker Timothy Clark LOWER_WALLS BIASVALUE WHOLEMOLECULES CENTER CONSTANT MATHEVAL PRINT UPPER_WALLS METAD DISTANCE vatom generic function colvar bias
23.028 Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process chemistry Ammonia decomposition; Dynamics;OPES; Neural Network potential Manyi Yang LOWER_WALLS COORDINATIONNUMBER CONTACT_MATRIX FLUSH PRINT ONES MEAN ENERGY DISTANCES SUM OPES_METAD MATRIX_VECTOR_PRODUCT MATHEVAL ZDISTANCES FIXEDATOM GROUP DISTANCE CUSTOM UNITS COM UPPER_WALLS LESS_THAN COMMITTOR vatom generic multicolvar opes core adjmat function colvar matrixtools bias symfunc setup
23.022 A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar methods collective variables, machine learning, toy model Enrico Trizio LOWER_WALLS POSITION OPES_METAD BIASVALUE CUSTOM UNITS PRINT UPPER_WALLS PYTORCH_MODEL ENDPLUMED generic opes colvar function pytorch bias setup
23.021 Into the Dynamics of Rotaxanes at Atomistic Resolution materials metadynamics, rotaxanes, molecular shuttles, molecular machines Luigi Leanza CUSTOM TORSION CENTER MATHEVAL PRINT UPPER_WALLS FIXEDATOM METAD DISTANCE vatom generic function colvar bias
23.016 Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action bio G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics Timothy Clark REWEIGHT_METAD DUMPGRID WHOLEMOLECULES HISTOGRAM RMSD MATHEVAL MOLINFO PRINT READ METAD DISTANCE CONVERT_TO_FES generic function colvar bias gridtools
22.029 Angiotensin-1-7_Metadynamics bio Metadynamics, Angiotensin-(1-7), peptide L.-América Chi LOWER_WALLS WHOLEMOLECULES COORDINATION FLUSH PRINT UPPER_WALLS GYRATION METAD GROUP bias core colvar generic
22.008 Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters materials Well tempered metadynamics, ab-initio, ase Daniel Sucerquia COMBINE LOWER_WALLS COORDINATIONNUMBER ONES MEAN CUSTOM MATRIX_VECTOR_PRODUCT COORDINATION FLUSH UNITS CONTACT_MATRIX UPPER_WALLS COM GYRATION METAD GROUP DISTANCE vatom generic core adjmat function colvar matrixtools bias symfunc setup
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 COMBINE METAD LESS_THAN SECONDARY_STRUCTURE_RMSD CUSTOM ANGLE TORSION WHOLEMOLECULES COORDINATION FLUSH CONSTANT ALPHABETA MOLINFO UPPER_WALLS PRINT SUM DISTANCE ALPHARMSD generic multicolvar secondarystructure function colvar bias
22.006 Peptide framework for screening the effects of amino acids on assembly bio metadynamics, peptides Andrew White COMBINE DISTANCE DUMPGRID MEAN HISTOGRAM INCLUDE DISTANCES COM PRINT GYRATION METAD GROUP REWEIGHT_BIAS CONVERT_TO_FES vatom generic multicolvar core function colvar bias gridtools
22.004 Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques chemistry reaction discovery, OPES, collective variables Umberto Raucci LOWER_WALLS OPES_METAD LOAD CUSTOM COORDINATION UNITS MATHEVAL PYTORCH_MODEL COM UPPER_WALLS OPES_METAD_EXPLORE PRINT GROUP DISTANCE vatom generic opes core function colvar pytorch bias setup
21.047 Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations materials pair entropy, metadynamics, ves, solids, crystallization Pablo Piaggi COMBINE METAD VOLUME LOAD TD_WELLTEMPERED OPT_AVERAGED_SGD PAIRENTROPY VES_LINEAR_EXPANSION ENERGY PRINT RESTART BF_LEGENDRE ves generic function colvar bias gridtools setup
21.043 Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes chemistry well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability Huixia Lu TORSION PRINT FIXEDATOM METAD FIT_TO_TEMPLATE bias colvar vatom generic
21.041 Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics methods metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions Matej Badin COMBINE VOLUME CUSTOM COORDINATION PRINT ENDPLUMED METAD bias function colvar generic
21.027 EGFR activating mutations mechanism bio metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA Francesco Gervasio LOWER_WALLS LESS_THAN SECONDARY_STRUCTURE_RMSD WHOLEMOLECULES SUM INCLUDE MATHEVAL MOLINFO CONTACTMAP UPPER_WALLS ENERGY PRINT METAD DISTANCE ALPHARMSD generic secondarystructure function colvar bias
21.026 Probing allosteric regulations with coevolution-driven molecular simulations bio metadynamics, coevolution, allostery, adenylate cyclase Francesco Colizzi PATHMSD WHOLEMOLECULES UNITS PRINT COM UPPER_WALLS METAD DISTANCE vatom generic colvar bias setup
21.014 how to determine statistically accurate conformational ensembles bio metadynamics, metainference, errors, cv, SAXS, ensemble determination Cristina Paissoni COMBINE ANTIBETARMSD PRINT ENSEMBLE CONSTANT CONTACTMAP STATS GYRATION SUM SECONDARY_STRUCTURE_RMSD BIASVALUE METAD CUSTOM TORSION WHOLEMOLECULES CENTER PBMETAD ALPHABETA MOLINFO SAXS LESS_THAN vatom generic multicolvar secondarystructure function colvar isdb bias
21.001 Substrate recognition and catalysis by glycosaminoglycan sulfotransferases bio metadynamics, well-tempered metadynamics, puckering, coordination Tarsis Ferreira LOWER_WALLS REWEIGHT_METAD PUCKERING DUMPGRID WHOLEMOLECULES COORDINATION HISTOGRAM ENERGY INCLUDE PRINT UPPER_WALLS MOLINFO RANDOM_EXCHANGES METAD GROUP DISTANCE generic core colvar bias gridtools
20.033 COVID-19 Spike protein opening transition mechanism bio EMMI, CryoEM, COVID-19, Spike, Metainference Faidon Brotzakis BIASVALUE DUMPGRID WHOLEMOLECULES HISTOGRAM RMSD READ PRINT MOLINFO DISTANCES EMMI GROUP CONVERT_TO_FES generic multicolvar core colvar isdb bias gridtools
20.031 Soft fluorescent nanoshuttles targeting receptors chemistry polymers, receptors, nanoparticles, fluorescent probes Adriana Pietropaolo WHOLEMOLECULES COORDINATION CENTER PBMETAD PRINT bias colvar vatom generic
20.029 High Conformational Flexibility of the E2F1/DP1/DNA complex bio SAXS, protein-DNA complex, hySAXS, ensemble determination Cristina Paissoni BIASVALUE WHOLEMOLECULES CENTER ENSEMBLE INCLUDE MOLINFO PRINT SAXS STATS RESTRAINT GROUP DISTANCE vatom generic core function isdb colvar bias
20.009 The dynamics of linear polyubiquitin bio saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics Carlo Camilloni COMBINE METAINFERENCE CUSTOM TORSION WHOLEMOLECULES CENTER ENSEMBLE CONSTANT ALPHABETA MOLINFO SAXS STATS GYRATION PBMETAD FLUSH SUM PRINT DISTANCE vatom generic multicolvar function colvar isdb bias
19.075 PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python other Python, automatic differentiation Toni Giorgino COMBINE DISTANCE CUSTOM ANGLE TORSION CENTER PRINT RESTRAINT ENDPLUMED GROUP DUMPDERIVATIVES vatom generic core function colvar bias
19.067 Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways bio metadynamics, ligand unbinding Jakub Rydzewski LOWER_WALLS PATHMSD RESTART UNITS PRINT UPPER_WALLS METAD bias colvar generic setup
19.054 MetaFEP methods metadynamics, chemistry, free energy perturbation GiovanniMaria Piccini COMBINE LOWER_WALLS FLUSH UNITS ENERGY PRINT UPPER_WALLS METAD DISTANCE generic function colvar bias setup
19.052 Gibbs free energy of homogeneous nucleation materials nucleation, surface excess free energy Gareth Tribello METAD MORE_THAN CELL ONES MEAN CUSTOM FCCUBIC_FUNC MATRIX_VECTOR_PRODUCT CONTACT_MATRIX FCCUBIC UNITS PRINT UPPER_WALLS ENDPLUMED SUM GROUP generic core adjmat function colvar matrixtools bias symfunc setup
19.048 Understanding Ligand Binding Selectivity in a Prototypical GPCR Family bio metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding Francesco Gervasio LOWER_WALLS BIASVALUE WHOLEMOLECULES CONSTANT MATHEVAL PRINT COM UPPER_WALLS METAD DISTANCE vatom generic function colvar bias
19.040 Optimal Metric for Path Collective Variables bio metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path Francesco Luigi Gervasio TORSION MATHEVAL PRINT ENDPLUMED METAD bias colvar function generic
19.032 Chemical reaction in solution using path collective variables based on coordination patterns chemistry chemical reactions, solutions, metadynamics, coordination patterns Fabio Pietrucci METAD PATH FLUSH DISTANCES UPPER_WALLS PRINT RESTART generic multicolvar mapping bias setup
19.025 Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide bio metainference, NMR, protein dynamics, force-fields Carlo Camilloni METAINFERENCE RDC BIASVALUE CS2BACKBONE TORSION WHOLEMOLECULES FLUSH ENSEMBLE PBMETAD MOLINFO PRINT STATS GYRATION ENDPLUMED JCOUPLING generic isdb function colvar bias
19.023 RECT methods metadynamics, replica exchange Giovanni Bussi TORSION WHOLEMOLECULES PRINT GYRATION METAD bias colvar generic
19.016 Succinnic acid gamma polymorph materials Succinnic acid, conformers, polymorphs, metadynamics Matteo Salvalaglio COMBINE LOWER_WALLS VOLUME CELL TORSION ENERGY MATHEVAL PRINT UPPER_WALLS ENDPLUMED METAD bias function colvar generic
25.006 Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations methods Enhanced sampling, Atomistic simulations, Conformational ensemble, PROTACs, Targeted Protein Degradation, Chamelonic molecules Shikshya Bhusal, Omar Valsson READ CENTER INCLUDE GYRATION ENERGY PBMETAD RESTART TORSION VOLUME PRINT DISTANCE bias setup generic vatom colvar
25.002 M3_PCV-ABMD chemistry Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor Gian Marco Elisi ABMD PATHMSD UPPER_WALLS UNITS ENDPLUMED PRINT bias colvar setup 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 ENDPLUMED FLUSH INCLUDE MOLINFO GYRATION COORDINATION PARABETARMSD ANTIBETARMSD PBMETAD DIHCOR TORSION GROUP PRINT COMBINE DISTANCE ALPHARMSD bias multicolvar core generic secondarystructure function colvar
24.026 Constant pH metadynamics of RNA oligomers bio metadynamics, pH, RNA Giovanni Bussi MOLINFO PUCKERING RESTART TORSION METAD PRINT setup bias generic colvar
24.018 A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations chemistry prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning Léon HUET PRINT DISTANCE generic colvar
24.009 Weighted Shape Gaussian Mixture Models bio metadynamics, clustering Glen Hocky GROUP UNITS TORSION METAD PRINT bias setup core generic 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 WHOLEMOLECULES METAD SHADOW UPPER_WALLS CENTER CUSTOM POSITION MOLINFO WRAPAROUND DISTANCES FIT_TO_TEMPLATE GROUP PRINT DISTANCE SUM isdb bias multicolvar core generic vatom function colvar
23.027 CmuMD simulations of NaCl(aq) at NaCl chemistry CmuMD, DFS, Q3, Pair Entropy Aaron Finney DENSITY CONTACT_MATRIX UNITS FIXEDATOM DFSCLUSTERING LOAD AROUND CLUSTER_NATOMS RESTRAINT LOCAL_Q3 LOCAL_AVERAGE Q3 DUMPGRID HISTOGRAM COORDINATIONNUMBER GROUP PRINT CLUSTER_DISTRIBUTION clusters gridtools bias symfunc setup core volumes generic vatom adjmat
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 bias generic setup
23.018 Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention materials metadynamics, surface binding, peptide adsorption Kaylyn Torkelson UPPER_WALLS GYRATION COM PBMETAD PRINT DISTANCE bias colvar vatom generic
23.015 MPCs aggregation bio opes_explore, dimerization, MPCs, self-assembly Vikas Tiwari WHOLEMOLECULES METAD UPPER_WALLS CENTER CUSTOM LOWER_WALLS OPES_METAD_EXPLORE COORDINATION COM GROUP PRINT DISTANCE opes bias core generic vatom function colvar
23.007 Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains bio metadynamics, peptoids, parallel-bias metadynamics Jim Pfaendtner WHOLEMOLECULES INCLUDE GYRATION COORDINATION COM RESTRAINT PBMETAD TORSION PRINT vatom bias generic colvar
22.026 Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification materials Peptoid, silica Jim Pfaendtner UPPER_WALLS MOLINFO GYRATION COM PBMETAD PRINT DISTANCE bias generic colvar vatom
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 WHOLEMOLECULES METAD COM TORSION GROUP PRINT DISTANCE bias core generic vatom colvar
22.000 Amyloid precursor protein processing by human γ-secretase bio Bias Exchange Metadynamics, Helix unfolding, coupled binding Xiaoli Lu SUM UNITS CENTER INCLUDE MOLINFO COORDINATION ANTIBETARMSD RANDOM_EXCHANGES CONTACTMAP METAD PRINT LESS_THAN SECONDARY_STRUCTURE_RMSD DISTANCE ALPHARMSD bias setup generic vatom secondarystructure function colvar
21.023 Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling methods enhanced sampling, collective variables, machine learning Jakub Rydzewski CONSTANT UNITS CUSTOM INCLUDE ENERGY REWEIGHT_METAD TORSION BIASVALUE METAD PRINT DISTANCE bias setup generic function colvar
21.012 NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition bio funnel metadynamics Jim Pfaendtner FUNNEL UPPER_WALLS LOWER_WALLS COM FUNNEL_PS METAD PRINT DISTANCE bias generic vatom funnel colvar
21.011 CmuMD simulations of NaCl(aq) at graphite chemistry CmuMD, DFS clustering Aaron Finney DENSITY CONTACT_MATRIX FIXEDATOM DFSCLUSTERING LOAD AROUND MFILTER_MORE CLUSTER_NATOMS RESTRAINT DUMPGRID MULTICOLVARDENS COORDINATIONNUMBER GROUP PRINT CLUSTER_DISTRIBUTION clusters gridtools bias multicolvar symfunc setup core volumes generic vatom adjmat
21.006 OPES, On-the-fly Probability Enhanced Sampling Method methods opes, alanine dipeptide, well-tempered, multithermal, multiumbrella Michele Invernizzi ENDPLUMED ECV_MULTITHERMAL ENERGY ECV_UMBRELLAS_LINE TORSION OPES_EXPANDED PRINT OPES_METAD generic opes colvar
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 OPT_AVERAGED_SGD MEAN CONTACT_MATRIX UPPER_WALLS ENERGY MATRIX_VECTOR_PRODUCT MORE_THAN ECV_MULTITHERMAL_MULTIBARIC ECV_UMBRELLAS_LINE RESTART ENVIRONMENTSIMILARITY COMBINE Q6 VES_LINEAR_EXPANSION CUSTOM ONES SPHERICAL_HARMONIC OPES_EXPANDED BF_LEGENDRE MATHEVAL TD_UNIFORM VOLUME GROUP PRINT DISTANCE_MATRIX SUM envsim opes bias symfunc matrixtools ves colvar setup core generic function adjmat
20.028 Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane bio metadynamics, KRas-4B, anionic membrane Huixia Lu CENTER FIT_TO_TEMPLATE RESTART METAD PRINT DISTANCE bias setup generic vatom colvar
20.016 Predicting polymorphism in molecular crystals using orientational entropy materials metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy Pablo Piaggi METAD UPPER_WALLS CENTER LOAD INCLUDE VOLUME GROUP PRINT bias setup core generic vatom colvar
20.014 amyloid beta small molecule interaction bio intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta Gabriella Heller INCLUDE MOLINFO ANTIBETARMSD PBMETAD ENDPLUMED ENSEMBLE ALPHARMSD CS2BACKBONE PARABETARMSD DIHCOR METAINFERENCE TORSION COMBINE COORDINATION WHOLEMOLECULES FLUSH STATS GYRATION GROUP PRINT isdb bias multicolvar core generic secondarystructure function 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 OPT_AVERAGED_SGD MEAN CONTACT_MATRIX UPPER_WALLS MATRIX_VECTOR_PRODUCT OPT_DUMMY MORE_THAN RESTART ENVIRONMENTSIMILARITY COMBINE Q6 VES_LINEAR_EXPANSION CUSTOM ONES SPHERICAL_HARMONIC TD_WELLTEMPERED BF_LEGENDRE MATHEVAL VOLUME GROUP PRINT DISTANCE_MATRIX SUM envsim bias symfunc matrixtools ves setup colvar core generic function adjmat
20.003 Enhanced sampling of transition states methods Variationally Enhanced Sampling, Target distribution, Transition state, Enhanced Sampling, Nucleation, chemical reaction Jayashrita Debnath OPT_AVERAGED_SGD UNITS VES_LINEAR_EXPANSION LOAD POSITION ENERGY PRINT BF_LEGENDRE setup colvar ves generic
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 METAD MORE_THAN SUM CONTACT_MATRIX MEAN UPPER_WALLS ENDPLUMED LOWER_WALLS GYRATION DISTANCES ENERGY ONES COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT GROUP PRINT DISTANCE LOWEST bias multicolvar symfunc colvar matrixtools core generic function adjmat
19.064 Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations materials metadynamics, peptide-surface binding Jim Pfaendtner UPPER_WALLS MOLINFO GYRATION ENERGY COM METAD PRINT DISTANCE bias generic colvar vatom
19.056 maze methods maze, ligand unbinding Jakub Rydzewski UNITS POSITION MAZE_LOSS MAZE_OPTIMIZER_BIAS PRINT MAZE_SIMULATED_ANNEALING colvar setup maze generic
19.055 Flying Gaussian method methods flying Gaussians, alanine dipeptide, peptide bond, Met-enkephalin Vojtech Spiwok MATHEVAL TORSION METAD PRINT COMBINE DISTANCE bias function colvar generic
19.049 Determining the sizes of solid/liquid clusters in MD trajectories of nucleation methods nucleation, metadynamics, clustering, Steinhardt order parameters Gareth Tribello METAD MORE_THAN CLUSTER_PROPERTIES CONTACT_MATRIX DFSCLUSTERING CUSTOM CLUSTER_DISTRIBUTION LOCAL_Q6 CLUSTER_NATOMS DISTANCES ONES OUTER_PRODUCT MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER SMAC OUTPUT_CLUSTER PRINT Q6 clusters bias symfunc multicolvar matrixtools generic function adjmat
19.030 Coarse-Grained MetaDynamics (CG-MetaD) bio Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy Vittorio Limongelli WHOLEMOLECULES UPPER_WALLS LOWER_WALLS COM METAD PRINT DISTANCE bias colvar generic vatom
19.029 WTE-metaD of FF domain of URNF1 C57D variant bio metadynamics, mutations, post-translational modification, ff domain Elena Papaleo WHOLEMOLECULES METAD UPPER_WALLS CONSTANT CUSTOM LOWER_WALLS MOLINFO GYRATION TORSION GROUP PRINT COMBINE ALPHABETA SUM bias multicolvar core generic function colvar
19.028 pRAVE methods RAVE, reaction coordinate, deep learning, metadynamics, kinetics Pratyush Tiwary WHOLEMOLECULES ALPHABETA COMMITTOR CONSTANT CUSTOM COM TORSION EXTERNAL RESTART PRINT COMBINE DISTANCE SUM bias multicolvar setup generic vatom function colvar
19.014 MIL101(Cr) SBUs assembly materials MOFs, nucleation, self-assembly, metadynamics Matteo Salvalaglio METAD MORE_THAN CONTACT_MATRIX MEAN ENDPLUMED GYRATION DISTANCES LOWEST ONES COORDINATIONNUMBER RESTART MATRIX_VECTOR_PRODUCT GROUP PRINT DISTANCE SUM bias multicolvar symfunc colvar setup matrixtools core generic function adjmat
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 MOVINGRESTRAINT DISTANCE METAD RESTRAINT MOLINFO TORSION RESTART PRINT PUCKERING colvar bias setup generic
24.030 NMR guided simulation of dsRBD bio Metainference, NMR, protein dynamics Debadutta Patra FLUSH CONSTANT SUM COMBINE ENSEMBLE DISTANCE GROUP WHOLEMOLECULES METAINFERENCE MOLINFO CUSTOM RDC STATS TORSION ALPHABETA PRINT colvar multicolvar generic function core isdb
24.022 Integrating Path Sampling with Enhanced Sampling for Rare-event Kinetics methods OPES Flooding, Weighted Ensemble, Metadynamics, Kinetics, Infrequent Metadynamics, Integrated Sampling Dhiman Ray GROUP UPPER_WALLS TORSION OPES_METAD MATHEVAL FIT_TO_TEMPLATE DISTANCE COMMITTOR ANGLE FIXEDATOM COMBINE WHOLEMOLECULES METAD CONTACTMAP CENTER PRINT ENDPLUMED RMSD COORDINATION MOLINFO CUSTOM colvar generic core opes function vatom bias
24.016 Cryo-EM guided simulations of ribozyme bio metainference, cryo-EM Giovanni Bussi BIASVALUE GROUP WHOLEMOLECULES MOLINFO EMMIVOX RESTRAINT ERMSD PRINT INCLUDE colvar generic core isdb bias
24.015 nanocluster QM/MM chemistry nanocluster, QM/MM, pathCV, OPES, reaction modelling Vikas Tiwari FLUSH DISTANCE COMMITTOR UPPER_WALLS RESTRAINT UNITS LOWER_WALLS CENTER PRINT OPES_METAD colvar setup generic opes vatom bias
24.008 yCD Metadynamics bio volume-based MetaD, path CVs, infrequent MetaD, product release James McCarty GROUP UPPER_WALLS INCLUDE MATHEVAL DUMPGRID FIT_TO_TEMPLATE DISTANCE COMMITTOR READ FIXEDATOM CONVERT_TO_FES COMBINE PATH WHOLEMOLECULES REWEIGHT_METAD METAD CONTACTMAP WRAPAROUND PRINT ENDPLUMED RMSD FLUSH COM MOLINFO COORDINATION HISTOGRAM GPATH colvar generic core function gridtools mapping vatom bias
23.037 Estimating binding free energy of solid binding peptides without extensive sampling bio metadynamics, solid binding peptides Xin Qi COM DISTANCE GYRATION UPPER_WALLS MOLINFO LOWER_WALLS PRINT PBMETAD vatom colvar bias 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 RMSD DISTANCE WHOLEMOLECULES REWEIGHT_METAD METAD MOLINFO READ HISTOGRAM CONVERT_TO_FES PRINT MATHEVAL DUMPGRID colvar generic function gridtools bias
23.003 Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations methods metadynamics, alchemical variable, alchemical free energy calculations Wei-Tse Hsu EXTRACV METAD PUT READ TORSION PRINT core colvar bias generic
23.000 Atomistic simulations of RNA tetraloop folding via PTWTE-WTM bio parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding Gül Zerze WHOLEMOLECULES UPPER_WALLS METAD LOWER_WALLS ENERGY CONTACTMAP PRINT colvar bias generic
22.036 Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction bio Well-tempered MetaDynamics with Hamiltonian Replica Exchange Miroslav Krepl FLUSH GHBFIX COMBINE BIASVALUE LOAD GROUP UPPER_WALLS METAD MOLINFO COORDINATION CUSTOM PRINT colvar setup generic function core bias
22.016 Homogeneous ice nucleation in an ab initio machine learning model of water chemistry ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces Pablo Piaggi DISTANCE_MATRIX SUM MORE_THAN GROUP ONES UPPER_WALLS ENERGY MATRIX_VECTOR_PRODUCT CUSTOM PRINT AROUND RESTART HISTOGRAM VOLUME ENVIRONMENTSIMILARITY OPES_METAD MEAN DUMPGRID volumes colvar setup matrixtools generic function core envsim opes adjmat gridtools bias
22.005 Collective Variable for Metadynamics Derived from AlphaFold Output bio AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable Vojtech Spiwok WHOLEMOLECULES METAD LOAD PRINT bias setup 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 DISTANCE UPPER_WALLS METAD LOWER_WALLS UNITS CUSTOM TORSION PRINT colvar setup generic function vatom bias
21.038 Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics materials metadynamics, SGOOP, nucleation, urea Ziyue Zou COMBINE VOLUME LOAD COORDINATIONNUMBER GROUP ONES METAD ENERGY MATRIX_VECTOR_PRODUCT CONTACT_MATRIX CENTER PRINT INCLUDE MEAN colvar setup symfunc matrixtools generic function core adjmat vatom bias
21.035 CmuMD simulations of NaCl(aq) at NaCl chemistry CmuMD, interface Aaron Finney LOAD DISTANCE GROUP RESTRAINT FIXEDATOM PRINT colvar setup generic core vatom bias
21.033 Multiple-path-metadynamics applied to DNA base-pairing transitions bio path-CV, metadynamics, multiple-walker, dna Alberto Pérez-de-Alba-Ortíz CONSTANT COMBINE MOVINGRESTRAINT UPPER_WALLS METAD RESTRAINT PRINT INCLUDE function bias generic
21.028 From Enhanced Sampling to Reaction Profiles methods collective variables, multi-state, machine learning, Deep-TDA Enrico Trizio GROUP UPPER_WALLS TORSION OPES_METAD MATHEVAL LOAD FIT_TO_TEMPLATE DISTANCE LOWER_WALLS ANGLE FIXEDATOM WHOLEMOLECULES UNITS PYTORCH_MODEL CENTER PRINT ENDPLUMED DISTANCES COORDINATION colvar setup pytorch multicolvar generic core opes function vatom bias
21.003 aSYN SAXS metainference bio metainference, SAXS Kresten Lindorff-Larsen FLUSH BIASVALUE SAXS GROUP WHOLEMOLECULES METAINFERENCE MOLINFO PBMETAD CENTER EEFSOLV ALPHARMSD PRINT GYRATION colvar generic core secondarystructure isdb vatom bias
21.000 Uremic toxin time scale dynamics bio uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) Jim Pfaendtner COM DISTANCE GROUP WHOLEMOLECULES PRINT vatom colvar core generic
20.022 Unified Approach to Enhanced Sampling methods OPES, expanded ensembles, importance sampling Michele Invernizzi ECV_MULTITHERMAL_MULTIBARIC GROUP ONES UPPER_WALLS CONTACT_MATRIX TORSION ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY SPHERICAL_HARMONIC MATHEVAL MORE_THAN LOAD Q6 ENERGY VOLUME MEAN DISTANCE_MATRIX ECV_MULTITHERMAL COMBINE WHOLEMOLECULES UNITS PRINT ENDPLUMED RMSD SUM OPES_EXPANDED ECV_LINEAR MOLINFO MATRIX_VECTOR_PRODUCT CUSTOM POSITION colvar symfunc setup matrixtools generic core opes envsim function adjmat bias
19.079 Impact of Glutamate Carboxylation in the Adsorption of the alpha-1 Domain of Osteocalcin to Hydroxyapatite and Titania bio metadynamics, peptide adsorption, parallel tempering, well-tempered ensemble Sarah Alamdari COM DISTANCE GROUP UPPER_WALLS METAD MOLINFO ENERGY PRINT GYRATION colvar generic core vatom bias
19.077 Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations materials metadynamics, peptide-surface binding Jim Pfaendtner COM DISTANCE UPPER_WALLS METAD MOLINFO ENERGY PRINT GYRATION vatom colvar bias generic
19.074 Asymmetric base pair opening in nucleic acids bio double helix, DNA, RNA, unwindability Giovanni Bussi DISTANCE WHOLEMOLECULES RESTRAINT COORDINATION LOWER_WALLS ENDPLUMED colvar bias generic
19.059 cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide bio bias-exchange metadynamics, cis-trans isomerization Fabrizio Marinelli METAD TORSION PRINT INCLUDE RANDOM_EXCHANGES colvar bias generic
19.051 Solid liquid interfacial free energy out of equilibrium materials metadynamics, nucleation, surface excess free energy Gareth Tribello CELL GROUP ONES UPPER_WALLS CONTACT_MATRIX LESS_THAN MORE_THAN LOWER_WALLS AROUND MEAN METAD UNITS PRINT ENDPLUMED FCCUBIC_FUNC SUM MATRIX_VECTOR_PRODUCT CUSTOM FCCUBIC volumes colvar setup symfunc matrixtools generic core function adjmat bias
19.038 native state dynamics of human and mouse b2m bio metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation Carlo Camilloni CONSTANT GROUP UPPER_WALLS TORSION ALPHABETA LESS_THAN BIASVALUE LOWER_WALLS RESTART SECONDARY_STRUCTURE_RMSD COMBINE WHOLEMOLECULES PRINT PBMETAD ENDPLUMED FLUSH SUM ANTIBETARMSD MOLINFO CUSTOM CS2BACKBONE colvar setup multicolvar generic core function secondarystructure isdb bias
19.027 Multithermal-multibaric simulations using VES methods ves, Wang Landau, multicanonical, liquid sodium, density anomaly Pablo Piaggi ACCUMULATE VES_LINEAR_EXPANSION DUMPGRID OPT_AVERAGED_SGD ENERGY READ RESTART TD_MULTICANONICAL CONVERT_TO_FES AVERAGE COMBINE BF_LEGENDRE UNITS OPT_DUMMY PRINT REWEIGHT_BIAS REWEIGHT_TEMP_PRESS CUSTOM HISTOGRAM colvar setup generic function gridtools ves bias
19.012 Martini-Beads multi-scale SAXS methods metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex Carlo Camilloni RMSD BIASVALUE SAXS DISTANCE GROUP WHOLEMOLECULES UPPER_WALLS MOLINFO RESTRAINT CENTER STATS PRINT INCLUDE ENDPLUMED colvar generic core function isdb vatom bias
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 RESTRAINT GROUP COMBINE PRINT DISTANCE CONTACT_MATRIX FIXEDATOM UNITS LOWER_WALLS CUSTOM FLUSH SUM COM UPPER_WALLS COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT MEAN LOWEST ONES METAD ANGLE COORDINATION DISTANCES generic colvar setup core multicolvar vatom function adjmat bias matrixtools symfunc