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
25.028	Designing transferable transition state guided collective variable via interpretable machine learning model for enhanced sampling. A case study on polymer collapse transition	bio	metadynamics, polymer collapse transition, transferable CV,interpretable ML-model	Saikat Dhibar and Biman Jana	GYRATION UPPER_WALLS CENTER COORDINATION METAD LOWER_WALLS PRINT COMBINE WHOLEMOLECULES DISTANCE MATHEVAL GROUP	function colvar vatom core bias generic
25.025	Enhanced Sampling of Ligand Binding Coupled to RNA Conformational Dynamics	bio	OPES, OPES Flooding , Metadynamics, RNA, Ligand binding, Free Energy, Kinetics, Funnel	Revanth Elangovan and Dhiman Ray	FUNNEL_PS UPPER_WALLS CENTER FUNNEL WRAPAROUND TORSION RMSD COORDINATION CUSTOM LOWER_WALLS COM METAD PRINT WHOLEMOLECULES COMMITTOR GROUP OPES_METAD MATHEVAL	function opes colvar vatom funnel bias core generic
25.023	Molecular simulations of Tau-protein oligomers	bio	metadynamics, proteins, aggregation	Giovanni Bussi	RMSD METAD CUSTOM FLUSH CONTACTMAP PRINT RESTART RESTRAINT	function colvar setup bias generic
25.006	Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations	methods	Enhanced sampling, Atomistic simulations, Conformational ensemble, PROTACs, Targeted Protein Degradation, Chamelonic molecules	Shikshya Bhusal, Omar Valsson	GYRATION VOLUME CENTER TORSION MOLINFO INCLUDE DUMPATOMS UPDATE_IF PRINT READ WHOLEMOLECULES DISTANCE RESTART ENERGY PBMETAD	colvar setup vatom bias generic
24.033	Transient interactions between the fuzzy coat and the cross-b core of brain-derived Ab42 filaments	bio	CryoEM, MEMMI, Metadynamics, Metainference, Ab42 Fibrils, structural ensemble	Maria Milanesi	ALPHARMSD UPPER_WALLS CENTER EMMI COM RMSD MOLINFO COORDINATION PARABETARMSD DUMPATOMS DUMPMASSCHARGE PRINT BIASVALUE WHOLEMOLECULES DISTANCE GROUP PBMETAD	isdb colvar secondarystructure vatom core bias generic
24.011	Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble	methods	committor, machine learning	Peilin Kang	TORSION POSITION LOWER_WALLS BIASVALUE MATHEVAL RMSD ENDPLUMED WHOLEMOLECULES ENERGY UPPER_WALLS COORDINATION MOLINFO INCLUDE LOAD PRINT UNITS DISTANCE GROUP CUSTOM CELL	function colvar setup core bias generic
24.003	Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations	chemistry	steered molecular dynamics, foldamers, peptoids, bio-inspired	Kaylyn Torkelson	GYRATION COM TORSION INCLUDE COORDINATION MOVINGRESTRAINT PRINT WHOLEMOLECULES DISTANCE ALPHABETA	colvar vatom bias multicolvar generic
23.044	Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition	materials	metadynamics, interlocked molecules	Luigi Leanza	COORDINATION METAD ENDPLUMED HISTOGRAM PRINT DUMPGRID READ CONVERT_TO_FES COMMITTOR GROUP	colvar core bias gridtools generic
23.036	Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water?	bio	NaCl, nucleation, metadynamics	Ruiyu Wang	VOLUME METAD Q4 COORDINATIONNUMBER COMBINE PRINT Q6 MATHEVAL ENERGY	function colvar bias symfunc generic
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	COORDINATION MOLINFO METAD ERMSD PRINT COMBINE BIASVALUE WHOLEMOLECULES GHBFIX	colvar bias function generic
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 ANN FIT_TO_TEMPLATE POSITION METAD MOLINFO PRINT COMBINE WHOLEMOLECULES	function colvar secondarystructure annfunc bias generic
23.023	Rational design of novel biomimetic sequence-defined polymers for mineralization applications	methods	metadynamics, surface binding, biomimetic mineralization	Kaylyn Torkelson	GYRATION UPPER_WALLS COM COORDINATION PRINT DISTANCE PBMETAD	colvar generic bias vatom
23.014	Structural basis of dimerization of chemokine receptors CCR5 and CXCR4	bio	metadynamics, oligomerization, chemokine receptors, GPCR, membrane	Vittorio Limongelli	UPPER_WALLS COM TORSION METAD FLUSH PRINT COMBINE WHOLEMOLECULES DISTANCE	function colvar vatom bias generic
23.010	An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands	bio	GPCR, binding free energy, free energy surface	Timothy Clark	UPPER_WALLS METAD LOWER_WALLS PRINT BIASVALUE WHOLEMOLECULES DISTANCE MATHEVAL CONSTANT	colvar bias function generic
22.041	Skipping the Replica Exchange Ladder with Normalizing Flows	methods	OPES, alanine, normalizing flows, replica exchange	Michele Invernizzi	ECV_MULTITHERMAL TORSION POSITION ENDPLUMED OPES_EXPANDED PRINT UNITS ENERGY OPES_METAD	colvar generic setup opes
22.027	Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain	Max Bonomi	PRINT RMSD	colvar generic
22.016	Homogeneous ice nucleation in an ab initio machine learning model of water	chemistry	ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces	Pablo Piaggi	UPPER_WALLS VOLUME CUSTOM HISTOGRAM ENVIRONMENTSIMILARITY AROUND PRINT DUMPGRID RESTART ENERGY OPES_METAD	volumes function opes colvar setup envsim bias gridtools generic
22.000	Amyloid precursor protein processing by human γ-secretase	bio	Bias Exchange Metadynamics, Helix unfolding, coupled binding	Xiaoli Lu	ALPHARMSD CENTER ANTIBETARMSD COORDINATION INCLUDE MOLINFO METAD CONTACTMAP RANDOM_EXCHANGES PRINT UNITS DISTANCE	colvar secondarystructure vatom setup bias generic
21.038	Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics	materials	metadynamics, SGOOP, nucleation, urea	Ziyue Zou	VOLUME CENTER INCLUDE METAD LOAD PRINT COMBINE COORDINATIONNUMBER ENERGY GROUP	function colvar setup vatom core bias symfunc generic
21.037	Molecular Dynamics simulations of RBD/hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain	Max Bonomi	PRINT RMSD DISTANCE	colvar generic
21.036	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	ALPHARMSD GYRATION UPPER_WALLS ANTIBETARMSD COORDINATION MOLINFO METAD PARABETARMSD LOWER_WALLS RANDOM_EXCHANGES ENERGY PRINT DIHCOR WHOLEMOLECULES GROUP	colvar secondarystructure core bias multicolvar generic
20.029	High Conformational Flexibility of the E2F1/DP1/DNA complex	bio	SAXS, protein-DNA complex, hySAXS, ensemble determination	Cristina Paissoni	CENTER MOLINFO INCLUDE STATS SAXS PRINT BIASVALUE WHOLEMOLECULES DISTANCE GROUP ENSEMBLE RESTRAINT	isdb function colvar vatom core bias generic
20.028	Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane	bio	metadynamics, KRas-4B, anionic membrane	Huixia Lu	CENTER FIT_TO_TEMPLATE METAD PRINT RESTART DISTANCE	colvar setup vatom bias generic
20.025	The role of water in host-guest interaction	bio	ligand binding, water, opes, SAMPL5	Valerio Rizzi	UPPER_WALLS CENTER COORDINATION FIT_TO_TEMPLATE GROUP ENDPLUMED PRINT WHOLEMOLECULES DISTANCE FIXEDATOM PYTORCH_MODEL ENERGY OPES_METAD MATHEVAL ANGLE	function opes colvar vatom core bias pytorch generic
20.022	Unified Approach to Enhanced Sampling	methods	OPES, expanded ensembles, importance sampling	Michele Invernizzi	TORSION POSITION OPES_EXPANDED ECV_MULTITHERMAL_MULTIBARIC Q6 MATHEVAL ECV_MULTITHERMAL RMSD ENDPLUMED WHOLEMOLECULES ENERGY UPPER_WALLS MOLINFO LOAD PRINT ENVIRONMENTSIMILARITY UNITS ECV_LINEAR ECV_UMBRELLAS_LINE VOLUME CUSTOM	function opes colvar setup envsim bias symfunc generic
20.020	Parallel Bias Metadynamics	methods	pbmetad, trp-cage, folding	Max Bonomi	GYRATION COORDINATION INCLUDE MOLINFO PRINT DIHCOR WHOLEMOLECULES ALPHABETA PBMETAD	colvar multicolvar bias generic
20.012	Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies	bio	metadynamics, well-tempered ensemble, ligand binding, binding affinity calculations, novel COLVAR, funnel restraints, Hamiltonian replica-exchange, PathCV, COMetPath, SWISH	Francesco Gervasio	UPPER_WALLS COM INCLUDE METAD MOLINFO LOWER_WALLS CONTACTMAP LOAD PRINT PROJECTION_ON_AXIS BIASVALUE WHOLEMOLECULES DISTANCE MATHEVAL FUNCPATHGENERAL GROUP CONSTANT	function colvar setup vatom core bias generic
19.070	Unexpected Dynamics in the UUCG RNA Tetraloop	bio	well-tempered metadynamics, RNA, UUCG, maximum entropy	Sandro Bottaro	RMSD MOLINFO METAD TORSION ERMSD PRINT WHOLEMOLECULES DISTANCE	colvar bias generic
19.060	Neural networks-based variationally enhanced sampling	methods	ves, neural networks	Luigi Bonati	TORSION POSITION ENDPLUMED LOAD PRINT ENVIRONMENTSIMILARITY UNITS Q6 ENERGY	colvar setup envsim symfunc generic
19.050	Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes	chemistry	metadynamics, membranes, Willard Chandler surface	Gareth Tribello	UPPER_WALLS METAD DISTANCE_FROM_CONTOUR HISTOGRAM DUMPGRID READ CONVERT_TO_FES PRINT COMBINE RESTART REWEIGHT_BIAS	function setup bias contour gridtools generic
19.039	Funnel Metadynamics	bio	funnel-metadynamics, absolute binding free energy, ligand-receptor complexes	Vittorio Limongelli	FUNNEL_PS UPPER_WALLS FUNNEL COM RMSD METAD LOWER_WALLS PRINT WHOLEMOLECULES DISTANCE	colvar vatom funnel bias generic
19.038	native state dynamics of human and mouse b2m	bio	metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation	Carlo Camilloni	UPPER_WALLS ANTIBETARMSD MOLINFO FLUSH LOWER_WALLS ENDPLUMED PRINT CS2BACKBONE BIASVALUE WHOLEMOLECULES RESTART ALPHABETA GROUP PBMETAD	isdb secondarystructure setup core bias multicolvar generic
19.011	Automatic Gradient Computation for Collective Variables	other	gradient, differentiation, curvature	Toni Giorgino	ENDPLUMED	generic
25.021	All You Need Is Water. Converging Ligand Binding Simulations with Hydration Collective Variables	bio	OPES Explore, ligand binding, binding free energy, water, hydration CVs, SAMPL challenge, host-guest	Valerio Rizzi	OPES_METAD_EXPLORE WHOLEMOLECULES GROUP DISTANCE COORDINATION FIT_TO_TEMPLATE ANGLE MATHEVAL FIXEDATOM UPPER_WALLS ENERGY CENTER PRINT	colvar core opes vatom generic function bias
25.014	Atomic resolution ensembles of intrinsically disordered proteins with Alphafold	bio	bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement	Vincent Schnapka	BAIES GROUP BIASVALUE PRINT	generic bias core isdb
25.000	Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer	bio	metadynamics, pathCV	Sahithya Sridharan Iyer	METAD RESTART WHOLEMOLECULES GROUP MOLINFO DISTANCE COM FUNCPATHGENERAL UPPER_WALLS PRINT	colvar setup core vatom generic function bias
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	RESTART OPES_METAD GROUP LOWER_WALLS CUSTOM UNITS DISTANCE COORDINATION COMMITTOR UPPER_WALLS PRINT	colvar setup core opes generic function bias
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	OPES_METAD_EXPLORE WHOLEMOLECULES GROUP LOWER_WALLS DISTANCE COORDINATION TORSION FIT_TO_TEMPLATE ANGLE ENDPLUMED MATHEVAL FIXEDATOM UPPER_WALLS ECV_MULTITHERMAL ENERGY CENTER OPES_EXPANDED PRINT	colvar core opes vatom generic function bias
24.013	Estimating Free Energy Surfaces and their Convergence from multiple, independent static and history-dependent biased molecular-dynamics simulations with Mean Force Integration	methods	Mean Force Integration, Convergence, FES, Umbrella Sampling	Matteo Salvalaglio	METAD RESTART COORDINATIONNUMBER BIASVALUE DISTANCE MOLINFO COMMITTOR TORSION FLUSH RESTRAINT MATHEVAL ENERGY PRINT	colvar setup symfunc generic function bias
23.035	An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors	bio	G protein coupled receptor, peptide ligands, metadynamics, multiple-walker	Timothy Clark	METAD WHOLEMOLECULES LOWER_WALLS BIASVALUE DISTANCE CONSTANT MATHEVAL CENTER UPPER_WALLS PRINT	colvar vatom generic function bias
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	generic setup bias
23.020	FEP simulations of ATOX1 homodimer	chemistry	parallel bias metadynamics, FEP, free-energy of metal ion dissociation	Adriana Pietropaolo	WHOLEMOLECULES BIASVALUE DISTANCE CONSTANT ANGLE PBMETAD MATHEVAL PRINT	colvar function bias generic
23.016	Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action	bio	G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics	Timothy Clark	METAD DUMPGRID READ WHOLEMOLECULES MOLINFO DISTANCE HISTOGRAM REWEIGHT_METAD CONVERT_TO_FES MATHEVAL RMSD PRINT	colvar gridtools generic function bias
23.011	OneOPES, a combined enhanced sampling method to rule them all	bio	OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding	Valerio Rizzi	OPES_METAD_EXPLORE METAD MOLINFO DISTANCE ECV_MULTITHERMAL TORSION OPES_EXPANDED ENDPLUMED ENERGY PRINT	colvar generic opes bias
23.006	Transcription factor unbinding	bio	metadynamics, DNA, conformational changes	Malin Lüking	METAD DUMPFORCES DISTANCE MOLINFO CONTACTMAP ALPHARMSD COM ANGLE PRINT	colvar vatom generic secondarystructure bias
22.032	Reciprocal barrier restraint. Application to path-meta-eABF	methods	restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC	Istvan Kolossvary	METAD BIASVALUE CUSTOM PATHMSD DRR FLUSH PRINT	colvar drr generic function bias
22.030	Mixing physics across temperatures with generative artificial intelligence	methods	REMD, Generative AI, DDPM	Yihang Wang	TORSION WHOLEMOLECULES PRINT	colvar generic
22.026	Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification	materials	Peptoid, silica	Jim Pfaendtner	DISTANCE MOLINFO COM GYRATION PBMETAD UPPER_WALLS PRINT	bias colvar vatom generic
22.015	Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome	bio	photodynamics, bacteriophytochrome, variationally enhanced sampling	Jakub Rydzewski	TD_UNIFORM VES_LINEAR_EXPANSION TORSION OPT_AVERAGED_SGD BF_FOURIER PRINT	colvar ves generic
21.051	Automatic learning of hydrogen-bond fixes in an AMBER RNA force field	methods	force field, RNA	Giovanni Bussi	METAD WHOLEMOLECULES BIASVALUE MOLINFO COMBINE COORDINATION ERMSD PRINT	colvar function generic 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	METAD WHOLEMOLECULES GROUP LOWER_WALLS ALPHABETA GYRATION ENDPLUMED UPPER_WALLS PRINT	colvar core generic multicolvar bias
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	METAD COORDINATIONNUMBER LOWER_WALLS DISTANCE COMBINE COORDINATION UPPER_WALLS PRINT	colvar symfunc generic function bias
21.041	Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics	methods	metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions	Matej Badin	METAD CUSTOM COMBINE COORDINATION VOLUME ENDPLUMED PRINT	colvar function generic bias
21.034	Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics	bio	reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics	Dongdong Wang	METAD INCLUDE TORSION PBMETAD RANDOM_EXCHANGES ENDPLUMED PRINT	colvar generic bias
21.027	EGFR activating mutations mechanism	bio	metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA	Francesco Gervasio	METAD INCLUDE WHOLEMOLECULES LOWER_WALLS MOLINFO DISTANCE CONTACTMAP ALPHARMSD MATHEVAL UPPER_WALLS ENERGY PRINT	colvar generic secondarystructure function bias
21.022	Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly	materials	parallel bias metadynamics, adsorption, peptide	Xin Qi	LOWER_WALLS DISTANCE MOLINFO COM GYRATION PBMETAD UPPER_WALLS ENERGY PRINT	colvar generic vatom bias
21.012	NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition	bio	funnel metadynamics	Jim Pfaendtner	METAD LOWER_WALLS DISTANCE COM FUNNEL_PS UPPER_WALLS FUNNEL PRINT	colvar funnel vatom generic bias
21.006	OPES, On-the-fly Probability Enhanced Sampling Method	methods	opes, alanine dipeptide, well-tempered, multithermal, multiumbrella	Michele Invernizzi	OPES_METAD ECV_UMBRELLAS_LINE ECV_MULTITHERMAL TORSION OPES_EXPANDED ENDPLUMED ENERGY PRINT	colvar opes generic
20.007	Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics	bio	metadynamics, loop movement, artificial intelligence	Pratyush Tiwary	METAD RESTART WHOLEMOLECULES DISTANCE COMBINE MOLINFO TORSION UPPER_WALLS RMSD PRINT	colvar setup generic function bias
20.002	Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study	bio	Metadynamics, path CVs	Riccardo Ocello	METAD RESTART WHOLEMOLECULES GROUP PATHMSD MOLINFO UPPER_WALLS PRINT	colvar setup core generic 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	CS2BACKBONE WHOLEMOLECULES GROUP BIASVALUE LOWER_WALLS MOLINFO ALPHABETA FLUSH PBMETAD ANTIBETARMSD ENDPLUMED UPPER_WALLS PRINT	isdb core generic secondarystructure multicolvar 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	METAD DUMPGRID READ LOWER_WALLS DISTANCE COMBINE COM HISTOGRAM ABMD REWEIGHT_METAD CONVERT_TO_FES ENDPLUMED MATHEVAL UPPER_WALLS PRINT	colvar gridtools vatom generic function bias
19.081	Calculation of phase diagrams in the multithermal-multibaric ensemble	methods	VES, variationally enhanced sampling, multithermal-multibaric, energy, Wang Landau, RefCV, kernel, bcc, fcc, sodium, aluminum	Pablo Piaggi	READ LOWER_WALLS COMBINE CELL TD_WELLTEMPERED MATHEVAL OPT_DUMMY LOAD PRINT REWEIGHT_TEMP_PRESS HISTOGRAM UPPER_WALLS RESTART Q6 VOLUME OPT_AVERAGED_SGD REWEIGHT_BIAS DUMPGRID TD_MULTITHERMAL_MULTIBARIC VES_LINEAR_EXPANSION BF_LEGENDRE CONVERT_TO_FES ENERGY	colvar setup gridtools symfunc generic ves function bias
19.080	Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium	methods	ves, variationally enhanced sampling, vibrational excitation, chemical reactions	Kristof Bal	DUMPGRID VES_LINEAR_EXPANSION LOWER_WALLS UNITS DISTANCE COMBINE COORDINATION HISTOGRAM ANGLE OPT_AVERAGED_SGD TD_WELLTEMPERED FLUSH CONVERT_TO_FES UPPER_WALLS BF_CHEBYSHEV TD_GRID PRINT EXTERNAL	colvar setup gridtools generic ves function bias
19.071	Time-independent free energies from metadynamics via Mean Force Integration	methods	metadynamics, mean force integration, MFI, thermodynamic integration	Matteo Salvalaglio	METAD READ DUMPGRID BIASVALUE DISTANCE COMMITTOR TORSION HISTOGRAM CONVERT_TO_FES REWEIGHT_BIAS MATHEVAL REWEIGHT_METAD EXTERNAL PRINT	colvar gridtools generic function bias
19.066	Finding ligand unbinding reaction pathways	methods	maze, ligand unbinding	Jakub Rydzewski	MAZE_OPTIMIZER_BIAS MAZE_SIMULATED_ANNEALING UNITS MAZE_LOSS PRINT POSITION	generic colvar setup maze
19.057	SAXS ensembles using Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics	Cristina Paissoni	STATS INCLUDE WHOLEMOLECULES GROUP ENSEMBLE BIASVALUE MOLINFO ALPHABETA COMBINE COORDINATION SAXS ANGLE PBMETAD ENDPLUMED MATHEVAL CENTER PRINT	colvar isdb core vatom generic function multicolvar bias
19.054	MetaFEP	methods	metadynamics, chemistry, free energy perturbation	GiovanniMaria Piccini	METAD LOWER_WALLS UNITS DISTANCE COMBINE FLUSH UPPER_WALLS ENERGY PRINT	colvar setup generic function bias
19.048	Understanding Ligand Binding Selectivity in a Prototypical GPCR Family	bio	metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	METAD WHOLEMOLECULES LOWER_WALLS BIASVALUE DISTANCE CONSTANT COM MATHEVAL UPPER_WALLS PRINT	colvar vatom generic function bias
19.036	Thermodynamics and kinetics of G protein-coupled receptor activation	bio	metadynamics, allostery, receptor conformation, GPCR, pharmacology	Davide Provasi	METAD WHOLEMOLECULES DISTANCE CONTACTMAP COM ENDPLUMED FUNCPATHMSD RMSD PRINT	colvar vatom generic function 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	GROUP DISTANCE COM TORSION RESTRAINT PRINT	colvar core vatom generic bias
19.022	eABF simulation of NANMA (alanine dipeptide)	methods	eABF, DRR, alanine dipeptide	Haochuan Chen	TORSION DRR PRINT	colvar generic drr
19.015	Ibuprofen conformational dynamics and thermodynamics surface	materials	Ibuprofen, crystal, surface, solvents, conformers, metadynamics	Matteo Salvalaglio	METAD LOWER_WALLS DISTANCE COMMITTOR TORSION CENTER UPPER_WALLS PRINT	colvar generic vatom bias
19.003	EMMI ClpP	bio	metainference, cryo-EM	Max Bonomi	GROUP BIASVALUE MOLINFO EMMI PRINT	isdb generic core bias
25.016	Advancing in silico drug design with Bayesian refinement of AlphaFold models	bio	bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment	Samiran Sen	BAIES GROUP BIASVALUE PRINT	core bias isdb generic
25.011	Chiral perovskite nucleation	chemistry	metadynamics, chiral perovskites, nucleation	Adriana Pietropaolo	DISTANCE UPPER_WALLS RESTART PRINT PBMETAD MULTI_RMSD UNITS LOWER_WALLS MATHEVAL	generic function setup bias colvar
25.010	Kinetic rates calculation with Ratchet&Pawl MD	methods	kinetics, ligand binding, ABMD, ratchet&pawl MD	Riccardo Capelli	DISTANCE PRINT COM GROUP COMMITTOR ABMD FLUSH WHOLEMOLECULES	generic vatom core bias colvar
24.029	Combination of OPES and OPES-Explore	methods	OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin	Dhiman Ray	PRINT COMBINE CONTACTMAP OPES_METAD_EXPLORE FIXEDATOM CENTER FLUSH UNITS CUSTOM WHOLEMOLECULES ENERGY BIASVALUE MOLINFO METAD DISTANCE UPPER_WALLS ENDPLUMED PYTORCH_MODEL GROUP POSITION MATHEVAL RMSD OPES_METAD INCLUDE FIT_TO_TEMPLATE COORDINATION LOWER_WALLS	generic vatom core opes function setup pytorch bias colvar
24.027	Proline cis and trans subensembles of a disordered peptide	bio	intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables	Alice Pettitt	DISTANCE GYRATION DIHCOR PBMETAD COMBINE PRINT ENDPLUMED INCLUDE TORSION WHOLEMOLECULES MOLINFO GROUP PARABETARMSD ANTIBETARMSD FLUSH COORDINATION ALPHARMSD	generic core secondarystructure function bias multicolvar colvar
24.021	Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state	chemistry	ion pairing, caco3, opes, proton transfer, crystallization	Pablo Piaggi	DISTANCE UPPER_WALLS ENERGY PRINT OPES_METAD COORDINATION	generic bias opes colvar
24.017	Absolute Binding Free Energies with OneOPES	methods	protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy	Francesco Gervasio	PRINT CONTACTMAP OPES_METAD_EXPLORE CONSTANT CUSTOM WHOLEMOLECULES WRAPAROUND ENERGY BIASVALUE PROJECTION_ON_AXIS OPES_EXPANDED MOLINFO METAD UPPER_WALLS RESTART TORSION GROUP MATHEVAL RMSD INCLUDE COM ECV_MULTITHERMAL COORDINATION LOWER_WALLS	generic vatom core opes function setup bias colvar
24.014	Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation	methods	data augmentation, geodesic interpolation, collective variables, protein folding	Juno Nam	UPPER_WALLS PRINT METAD RMSD PYTORCH_MODEL DRR WHOLEMOLECULES MOLINFO FLUSH COORDINATION LOWER_WALLS	generic drr pytorch bias colvar
23.039	Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation	chemistry	metadynamics, ligand dissociation	Eric Beyerle	DISTANCE DUMPMASSCHARGE UPPER_WALLS PRINT COMBINE FIXEDATOM RESTRAINT MOLINFO CENTER METAD	generic vatom function bias colvar
23.015	MPCs aggregation	bio	opes_explore, dimerization, MPCs, self-assembly	Vikas Tiwari	CUSTOM DISTANCE UPPER_WALLS PRINT OPES_METAD_EXPLORE CENTER GROUP COM COORDINATION METAD LOWER_WALLS WHOLEMOLECULES	generic vatom core opes function bias colvar
22.036	Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction	bio	Well-tempered MetaDynamics with Hamiltonian Replica Exchange	Miroslav Krepl	FLUSH UPPER_WALLS PRINT COMBINE BIASVALUE MOLINFO GHBFIX GROUP LOAD COORDINATION METAD CUSTOM	generic core function setup bias colvar
22.033	Reciprocal barrier restraint. Application to PROTAC passive permeability prediction	methods	PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR	Istvan Kolossvary	DISTANCE UNITS PRINT METAD BIASVALUE DRR COM FLUSH CUSTOM	generic drr vatom function setup bias 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	UPPER_WALLS RESTART PRINT PBMETAD RMSD EMMI BIASVALUE TORSION MOLINFO GROUP COM COORDINATION WHOLEMOLECULES	generic vatom core isdb setup bias colvar
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	DISTANCE LOWER_WALLS UPPER_WALLS COMBINE PRINT XANGLES ALPHABETA WHOLEMOLECULES TORSION MOLINFO COM YANGLES ZANGLES METAD CUSTOM MATHEVAL	generic vatom function bias multicolvar colvar
22.001	Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials	methods	enhanced sampling, variationally enhanced sampling, ves, metadynamics, bias representation, wavelets, adam	Benjamin Pampel	PRINT VES_OUTPUT_BASISFUNCTIONS BF_LEGENDRE BF_WAVELETS FLUSH UNITS ENERGY TD_WELLTEMPERED TD_UNIFORM BF_CUBIC_B_SPLINES METAD DISTANCE UPPER_WALLS OPT_AVERAGED_SGD VES_LINEAR_EXPANSION BF_CHEBYSHEV POSITION BF_GAUSSIANS INCLUDE OPT_ADAM COORDINATION	generic ves setup bias colvar
21.039	Deep learning the slow modes for rare events sampling	methods	collective variables, machine learning, slow modes, deep-tica, opes	Luigi Bonati	PRINT COMBINE CONTACTMAP FLUSH UNITS WHOLEMOLECULES ENERGY OPES_EXPANDED MOLINFO VOLUME ENVIRONMENTSIMILARITY DISTANCE ENDPLUMED PYTORCH_MODEL TORSION GROUP LOAD RMSD Q6 OPES_METAD INCLUDE ECV_MULTITHERMAL	generic symfunc core opes function setup envsim pytorch colvar
21.035	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, interface	Aaron Finney	DISTANCE PRINT FIXEDATOM RESTRAINT GROUP LOAD	generic vatom core setup bias colvar
21.029	Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs	bio	metadynamics, small peptide, machine learning	Pratyush Tiwary	ENERGY RESTART PRINT EXTERNAL TORSION MOLINFO FLUSH	generic bias setup colvar
21.020	Reweighted Jarzynski sampling	methods	free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions	Kristof Bal	HISTOGRAM PRINT COMBINE CONSTANT MOVINGRESTRAINT ANN UNITS FLUSH CUSTOM REWEIGHT_BIAS TD_WELLTEMPERED DUMPGRID BIASVALUE METAD DISTANCE UPPER_WALLS OPT_AVERAGED_SGD VES_LINEAR_EXPANSION LOAD BF_CHEBYSHEV REWEIGHT_METAD COORDINATIONNUMBER OPES_METAD RESTRAINT CONVERT_TO_FES	generic symfunc gridtools ves opes function setup bias annfunc colvar
21.016	MD SAXS GTPase associated center	bio	metadynamics, RNA, folding, SAXS	Giovanni Bussi	CUSTOM GYRATION UPPER_WALLS PRINT ERMSD INCLUDE MOLINFO GROUP SAXS METAD LOWER_WALLS WHOLEMOLECULES	generic core isdb function bias colvar
21.013	Role of vibrational excitation in heterogeneous catalysis	chemistry	catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption	Kristof Bal	HISTOGRAM COMBINE PRINT UNITS FLUSH REWEIGHT_BIAS DISTANCES DUMPGRID ANGLES UWALLS METAD DISTANCE UPPER_WALLS OPT_AVERAGED_SGD EXTERNAL VES_LINEAR_EXPANSION LOAD BF_CHEBYSHEV REWEIGHT_METAD COORDINATIONNUMBER RESTRAINT CONVERT_TO_FES TD_GRID COORDINATION LOWER_WALLS	generic symfunc gridtools ves function setup bias multicolvar colvar
21.001	Substrate recognition and catalysis by glycosaminoglycan sulfotransferases	bio	metadynamics, well-tempered metadynamics, puckering, coordination	Tarsis Ferreira	DISTANCE UPPER_WALLS ENERGY PRINT HISTOGRAM DUMPGRID INCLUDE RANDOM_EXCHANGES WHOLEMOLECULES MOLINFO GROUP PUCKERING COORDINATION METAD LOWER_WALLS REWEIGHT_METAD	generic core gridtools bias colvar
21.000	Uremic toxin time scale dynamics	bio	uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs)	Jim Pfaendtner	DISTANCE PRINT COM GROUP WHOLEMOLECULES	generic vatom colvar core
20.033	COVID-19 Spike protein opening transition mechanism	bio	EMMI, CryoEM, COVID-19, Spike, Metainference	Faidon Brotzakis	READ HISTOGRAM PRINT RMSD DUMPGRID DISTANCES EMMI BIASVALUE MOLINFO GROUP CONVERT_TO_FES WHOLEMOLECULES	generic core gridtools isdb bias multicolvar colvar
20.032	Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil	materials	clustering, conformational isomers	Matteo Salvalaglio	TORSION PRINT ENDPLUMED	generic colvar
20.019	Systematic finite-temperature reduction of crystal energy landscapes	materials	crystals, organics, structure prediction	Matteo Salvalaglio	UPPER_WALLS ENERGY PRINT VOLUME MATHEVAL METAD CELL LOWER_WALLS	generic function bias colvar
20.009	The dynamics of linear polyubiquitin	bio	saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics	Carlo Camilloni	ENSEMBLE DISTANCE GYRATION PBMETAD STATS PRINT ALPHABETA TORSION WHOLEMOLECULES MOLINFO CENTER SAXS FLUSH METAINFERENCE	generic vatom isdb function bias multicolvar colvar
19.072	SINE hairpin MD+NMR	bio	metadynamics, RNA, NMR	Giovanni Bussi	SORT DISTANCE PRINT METAD INCLUDE TORSION MAXENT MOLINFO COM WHOLEMOLECULES FLUSH COORDINATION MATHEVAL	generic vatom function bias colvar
19.063	Protein-ligand binding through metadynamics with path CVs	bio	metadynamics, path CVs, ligand binding	Mattia Bernetti	PATHMSD UPPER_WALLS PRINT METAD LOWER_WALLS WHOLEMOLECULES	generic bias colvar
19.043	Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	DISTANCE UNITS UPPER_WALLS RESTART COMBINE PRINT METAD DISTANCES FLUSH	generic function setup bias multicolvar colvar
19.017	Ligand binding pathways exploration	bio	metadynamics, ligand binding	Riccardo Capelli	WRAPAROUND READ UPPER_WALLS HISTOGRAM PRINT ENDPLUMED METAD POSITION DUMPGRID REWEIGHT_METAD FIT_TO_TEMPLATE WHOLEMOLECULES COM GROUP CONVERT_TO_FES FLUSH COORDINATION MATHEVAL	generic vatom core gridtools function bias colvar
19.016	Succinnic acid gamma polymorph	materials	Succinnic acid, conformers, polymorphs, metadynamics	Matteo Salvalaglio	CELL UPPER_WALLS ENERGY PRINT ENDPLUMED COMBINE TORSION VOLUME METAD LOWER_WALLS MATHEVAL	generic function bias colvar
19.001	RNA SHAPE	bio	metadynamics, RNA, ligand binding	Giovanni Bussi	FLUSH DISTANCE UPPER_WALLS COMBINE ANGLE PRINT DISTANCES ERMSD INCLUDE MOLINFO METAD LOWER_WALLS RANDOM_EXCHANGES	generic function bias multicolvar colvar
25.029	Energetic Constraints in the Enzymatic Depolymerization of Crystalline PET from enhanced molecular simulations	bio	HREX-Metadynamics, PETase, crystalline PET, amorphous PET, conformational ensembles, substrate binding, chain detachment	Ania Di Pede-Mattatelli and Francesco Colizzi	COM MOLINFO UNITS HISTOGRAM WHOLEMOLECULES DRMSD UPPER_WALLS METAD CONVERT_TO_FES PRINT DISTANCE RESTART ANGLE REWEIGHT_BIAS FIXEDATOM MOVINGRESTRAINT LOWER_WALLS DUMPGRID	vatom colvar setup gridtools bias generic
25.022	Imidazole Diffusion in SALEM-2 MOF	materials	OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials	Sudheesh Kumar Ethirajan	MOLINFO UNITS OPES_METAD WHOLEMOLECULES GROUP DISTANCE DISTANCES PROJECTION_ON_AXIS PRINT ENDPLUMED CENTER	vatom colvar setup core generic opes multicolvar
25.019	The Arch from the Stones. Understanding Protein Folding Energy Landscapes via Bio-inspired Collective Variables	bio	protein folding, OPES, OneOPES, binding free energy	Valerio Rizzi	MOLINFO ENERGY CUSTOM COMBINE OPES_METAD_EXPLORE OPES_EXPANDED GROUP COORDINATION DISTANCE PRINT ECV_MULTITHERMAL GHOST CENTER RMSD	vatom colvar core generic opes function
25.018	Metainference simulation for dimerization of RNA binding protein	bio	Metainference, Metadynamics, SAXS, protein dimer	Debadutta Patra	MOLINFO STATS WHOLEMOLECULES UPPER_WALLS GYRATION SAXS PBMETAD TORSION DISTANCE METAINFERENCE FLUSH PRINT ENSEMBLE CENTER	vatom colvar isdb bias generic function
24.030	NMR guided simulation of dsRBD	bio	Metainference, NMR, protein dynamics	Debadutta Patra	MOLINFO STATS WHOLEMOLECULES ALPHABETA RDC FLUSH GROUP METAINFERENCE PRINT DISTANCE ENSEMBLE	colvar isdb core generic function multicolvar
24.028	All-atom simulations of RNA-membrane interactions	bio	metadynamics, membrane, RNA	Giovanni Bussi	MOLINFO COMBINE POSITION WHOLEMOLECULES UPPER_WALLS GYRATION METAD GROUP PUCKERING DISTANCE PRINT DISTANCES MATHEVAL GHOST LOWER_WALLS CENTER SORT	vatom colvar core bias generic function multicolvar
24.008	yCD Metadynamics	bio	volume-based MetaD, path CVs, infrequent MetaD, product release	James McCarty	COM WHOLEMOLECULES MATHEVAL DISTANCE READ FIXEDATOM RMSD METAD GROUP PATH DUMPGRID HISTOGRAM FLUSH INCLUDE COORDINATION PRINT ENDPLUMED MOLINFO FIT_TO_TEMPLATE UPPER_WALLS REWEIGHT_METAD COMMITTOR CONVERT_TO_FES CONTACTMAP WRAPAROUND	vatom colvar core mapping gridtools bias generic function
23.046	Lasso Peptides - HLDA CV	bio	metadynamics, protein folding, HLDA, harmonic	Gabriel da Hora	UNITS WHOLEMOLECULES COMBINE METAD DISTANCE PRINT	colvar setup bias generic function
23.040	Supramolecular capsules assembly dynamics	chemistry	Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics	Riccardo Capelli	COM UNITS CUSTOM WHOLEMOLECULES POSITION FLUSH METAD GROUP DISTANCE PRINT DISTANCES CENTER	vatom colvar setup core bias generic function multicolvar
23.028	Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process	chemistry	Ammonia decomposition; Dynamics;OPES; Neural Network potential	Manyi Yang	COM UNITS ENERGY OPES_METAD ZDISTANCES UPPER_WALLS LOWER_WALLS CUSTOM FLUSH COMMITTOR GROUP DISTANCE PRINT DISTANCES FIXEDATOM MATHEVAL COORDINATIONNUMBER	vatom colvar function setup symfunc core bias generic opes multicolvar
23.018	Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention	materials	metadynamics, surface binding, peptide adsorption	Kaylyn Torkelson	COM UPPER_WALLS GYRATION PBMETAD DISTANCE PRINT	vatom generic colvar bias
23.013	Path meta-eABF simulation of large scale conformational change in STING protein	methods	meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint	Istvan Kolossvary	PATHMSD CUSTOM UNITS UPPER_WALLS DRR TIME FLUSH METAD PRINT LOWER_WALLS BIASVALUE	colvar setup bias generic function drr
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	HISTOGRAM LOWER_WALLS UPPER_WALLS OPES_EXPANDED ENVIRONMENTSIMILARITY PRINT ECV_UMBRELLAS_LINE RESTART DUMPGRID	setup gridtools bias generic opes envsim
23.000	Atomistic simulations of RNA tetraloop folding via PTWTE-WTM	bio	parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding	Gül Zerze	ENERGY WHOLEMOLECULES UPPER_WALLS METAD PRINT CONTACTMAP LOWER_WALLS	generic colvar bias
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 WHOLEMOLECULES GYRATION PBMETAD TORSION	generic colvar bias
22.029	Angiotensin-1-7_Metadynamics	bio	Metadynamics, Angiotensin-(1-7), peptide	L.-América Chi	WHOLEMOLECULES UPPER_WALLS GYRATION METAD GROUP FLUSH COORDINATION PRINT LOWER_WALLS	generic colvar bias core
21.052	On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets	materials	Ibuprofen, unbinding, WTmetaD	Matteo Salvalaglio	METAD COMMITTOR TORSION PRINT DISTANCE ENDPLUMED CENTER COORDINATIONNUMBER	vatom colvar symfunc bias generic
21.042	Peptoid-mediated Au nanocrystal growth	materials	parallel-bias metadynamics, peptoid, Au	Xin Qi	COM MOLINFO UPPER_WALLS GYRATION PBMETAD DISTANCE PRINT	vatom 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	LOWER_WALLS UPPER_WALLS PRINT DISTANCE	generic colvar bias
21.003	aSYN SAXS metainference	bio	metainference, SAXS	Kresten Lindorff-Larsen	MOLINFO WHOLEMOLECULES EEFSOLV ALPHARMSD GYRATION SAXS GROUP PBMETAD PRINT METAINFERENCE FLUSH CENTER BIASVALUE	vatom colvar secondarystructure isdb core bias 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	MOLINFO STATS WHOLEMOLECULES PRINT COORDINATION RESTRAINT	generic function colvar bias
20.017	FISST	methods	FISST, force, peptide, sampling, tempering	Glen Hocky	FISST UNITS ENERGY GYRATION GROUP DISTANCE PRINT RESTRAINT MATHEVAL BIASVALUE	colvar fisst setup core bias generic function
20.011	Uremic toxin analysis	bio	metadynamics, uremic toxin, serum albumin	Jim Pfaendtner	WHOLEMOLECULES GROUP COORDINATION DISTANCES DISTANCE PRINT RESTART CENTER	vatom colvar setup core generic multicolvar
19.068	Rethinking Metadynamics	methods	metadynamics, opes, convergence	Michele Invernizzi	UNITS OPES_METAD POSITION METAD TORSION PRINT ENDPLUMED EXTERNAL	colvar setup bias generic opes
19.067	Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways	bio	metadynamics, ligand unbinding	Jakub Rydzewski	PATHMSD UNITS UPPER_WALLS METAD PRINT RESTART LOWER_WALLS	generic colvar setup bias
19.064	Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	COM MOLINFO ENERGY UPPER_WALLS GYRATION METAD DISTANCE PRINT	vatom generic colvar bias
19.052	Gibbs free energy of homogeneous nucleation	materials	nucleation, surface excess free energy	Gareth Tribello	UNITS UPPER_WALLS METAD PRINT FCCUBIC ENDPLUMED CELL	colvar setup symfunc bias generic
19.045	Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water	materials	metadynamics, well-tempered, multiple walkers, LAMMPS	Marco De La Pierre	UNITS POSITION UPPER_WALLS FLUSH METAD GROUP COORDINATION PRINT RESTART LOWER_WALLS	colvar setup core bias 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	COM ENERGY UPPER_WALLS METAD DISTANCE PRINT	vatom generic 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	METAD TORSION PRINT ENDPLUMED MATHEVAL	generic colvar bias function
19.037	Scission free energy of organic dyes	chemistry	metadynamics, multiple walkers, matheval/lepton	Paolo Raiteri	UNITS UPPER_WALLS FLUSH METAD DISTANCE PRINT RESTART MATHEVAL	colvar setup bias generic function
19.030	Coarse-Grained MetaDynamics (CG-MetaD)	bio	Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy	Vittorio Limongelli	COM WHOLEMOLECULES UPPER_WALLS METAD DISTANCE PRINT LOWER_WALLS	vatom generic colvar bias
25.027	Enhanced-sampling MD simulations of a protein-peptide complex integrating SAXS and XL-MS experimental information	bio	steered MD, metadynamics, SAXS, XL-MS, ensemble reconstruction	Mattia Bernetti	GROUP WHOLEMOLECULES MOVINGRESTRAINT DISTANCE METAD CENTER SAXS GYRATION PRINT INCLUDE MOLINFO UPPER_WALLS	isdb core vatom colvar generic 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	FIXEDATOM RESTRAINT COMBINE FLUSH GROUP COORDINATIONNUMBER DISTANCE METAD DISTANCES ANGLE UPPER_WALLS PRINT COM LOWER_WALLS UNITS COORDINATION	core vatom multicolvar colvar setup generic function symfunc bias
24.026	Constant pH metadynamics of RNA oligomers	bio	metadynamics, pH, RNA	Giovanni Bussi	PUCKERING RESTART METAD PRINT TORSION MOLINFO	setup generic colvar bias
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 GROUP DISTANCE CENTER METAD UPPER_WALLS BIASVALUE GHBFIX PRINT MOLINFO COM LOWER_WALLS DEBUG COORDINATION	core vatom colvar generic function bias
24.009	Weighted Shape Gaussian Mixture Models	bio	metadynamics, clustering	Glen Hocky	GROUP METAD PRINT TORSION UNITS	core colvar setup generic bias
24.002	Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes	chemistry	metadynamics, ligand design, solvent extraction	Xiaoyu Wang	RESTART METAD PRINT TORSION UNITS	setup generic colvar bias
23.002	Critical comparison of general-purpose collective variables for crystal nucleation	methods	metadynamics, umbrella sampling, commitor, entropy, PIV	Julien Lam	LOCAL_AVERAGE RESTRAINT CUSTOM PIV PAIRENTROPY METAD VOLUME PRINT ENERGY Q6 UPPER_WALLS UNITS FUNCPATHMSD Q4	gridtools colvar setup generic function piv symfunc bias
22.003	Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling	methods	opes, metadynamics, reweighting, alanine, muller	Michele Invernizzi	CUSTOM PBMETAD LOWER_WALLS POSITION ENDPLUMED METAD OPES_METAD OPES_EXPANDED PRINT ECV_UMBRELLAS_FILE ENERGY BIASVALUE TORSION ECV_MULTITHERMAL OPES_METAD_EXPLORE UPPER_WALLS UNITS	opes colvar setup generic function bias
21.018	Localized Volume-based Metadynamics	bio	LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification	Riccardo Capelli	UPPER_WALLS HISTOGRAM MATHEVAL FLUSH WHOLEMOLECULES READ POSITION CONVERT_TO_FES REWEIGHT_METAD FIXEDATOM DISTANCE METAD DUMPGRID COM COORDINATION GROUP RMSD ENDPLUMED PRINT	core vatom gridtools colvar generic function bias
21.011	CmuMD simulations of NaCl(aq) at graphite	chemistry	CmuMD, DFS clustering	Aaron Finney	CONTACT_MATRIX FIXEDATOM RESTRAINT LOAD GROUP COORDINATIONNUMBER CLUSTER_NATOMS DUMPGRID CLUSTER_DISTRIBUTION DENSITY AROUND PRINT MULTICOLVARDENS DFSCLUSTERING MFILTER_MORE	adjmat core vatom gridtools multicolvar clusters setup generic volumes symfunc bias
19.062	Elucidating molecular design principles for charge-alternating peptides	bio	peptide folding, metadynamics, well-tempered ensemble, parallel tempering	Jim Pfaendtner	WHOLEMOLECULES METAD GYRATION PRINT ENERGY	generic colvar bias
19.061	Diffusion in porous materials	materials	metadynamics, porous materials, diffusion	Kim E. Jelfs	GROUP LOWER_WALLS RESTART DISTANCE CENTER METAD PRINT COM UPPER_WALLS	core vatom colvar setup generic bias
19.010	Multi-domain protein dynamics	bio	metainference, NMR, protein dynamics	Carlo Camilloni	ENSEMBLE DHENERGY RESTRAINT GROUP WHOLEMOLECULES DIHCOR PBMETAD RDC DISTANCE CENTER STATS ENDPLUMED PRINT TORSION MOLINFO ALPHABETA UPPER_WALLS METAINFERENCE	isdb core vatom multicolvar colvar generic function bias
19.000	VesDeltaF	methods	VES, convergence, suboptimal CVs	Michele Invernizzi	LOAD POSITION VES_DELTA_F ENDPLUMED METAD RESTART PRINT ENERGY TORSION UNITS	colvar setup generic ves bias
25.009	Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water	chemistry	metadynamics, nitrate photolysis	Kam-Tung Chan	READ COORDINATION UPPER_WALLS RESTART METAD REWEIGHT_METAD FLUSH DUMPGRID CUSTOM GROUP HISTOGRAM DISTANCE PRINT	function colvar generic setup bias core gridtools
24.018	A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations	chemistry	prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning	Léon HUET	DISTANCE PRINT	generic colvar
24.007	SWISH-X	bio	swish-x, SWISH-X, swish, expanded SWISH	Alberto Borsatto	ECV_MULTITHERMAL CONTACTMAP UPPER_WALLS INCLUDE WHOLEMOLECULES MOLINFO ENERGY OPES_EXPANDED PRINT	generic bias opes colvar
24.005	Learning Markovian Dynamics with Spectral Maps	methods	spectral map, collective variables, machine learning	Jakub Rydzewski	BIASVALUE CUSTOM UNITS DISTANCE PRINT	function colvar generic setup bias
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	WRAPAROUND UPPER_WALLS EMMIVOX INCLUDE BIASVALUE WHOLEMOLECULES GROUP MOLINFO DISTANCE PRINT	isdb colvar generic bias core
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	TORSION FIT_TO_TEMPLATE MATHEVAL ENDPLUMED MOLINFO LOWER_WALLS CENTER COORDINATION COM GROUP UNITS COMMITTOR PRINT WRAPAROUND OPES_METAD POSITION UPPER_WALLS BIASVALUE FLUSH OPES_METAD_EXPLORE WHOLEMOLECULES CUSTOM ENERGY DISTANCE	function vatom colvar generic setup opes bias core
23.026	Machine Learning Nucleation Collective Variables with Graph Neural Networks	chemistry	Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks	Florian Dietrich	Q6 LOWER_WALLS COORDINATIONNUMBER LOCAL_Q6 COMBINE METAD MFILTER_MORE MOVINGRESTRAINT GROUP PRINT	function symfunc generic multicolvar bias core
23.022	A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar	methods	collective variables, machine learning, toy model	Enrico Trizio	OPES_METAD LOWER_WALLS POSITION UPPER_WALLS BIASVALUE ENDPLUMED PYTORCH_MODEL CUSTOM UNITS PRINT	function colvar generic setup opes bias pytorch
23.021	Into the Dynamics of Rotaxanes at Atomistic Resolution	materials	metadynamics, rotaxanes, molecular shuttles, molecular machines	Luigi Leanza	FIXEDATOM TORSION CENTER UPPER_WALLS METAD MATHEVAL CUSTOM DISTANCE PRINT	function vatom colvar generic bias
22.037	Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site	chemistry	metadynamics, DNA, abasic	Mike Jones	DISTANCES DISTANCE METAD PRINT	generic bias multicolvar colvar
22.034	Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods	materials	metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene	Matteo Salvalaglio	LOWER_WALLS CELL UPPER_WALLS METAD DRMSD PRINT MATHEVAL CUSTOM COMMITTOR	function generic bias colvar
22.024	Conformational Entropy as a Potential Liability of Computationally Designed Antibodies	bio	metadynamics, conformational entropy, antibody, nanobody	Thomas Löhr	TORSION ALPHARMSD RESTART COM ANTIBETARMSD WHOLEMOLECULES ALPHABETA MOLINFO PBMETAD PRINT	secondarystructure vatom colvar generic setup multicolvar bias
22.018	Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations	bio	ligand binding, docking, EMMI, LAT1	Max Bonomi	EMMIVOX LOAD BIASVALUE WHOLEMOLECULES GROUP MOLINFO PRINT	isdb generic setup bias core
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	FIXEDATOM OPES_METAD LOWER_WALLS CENTER COORDINATION UPPER_WALLS RMSD COMMITTOR WHOLEMOLECULES FIT_TO_TEMPLATE MATHEVAL PYTORCH_MODEL CUSTOM GROUP DISTANCE PRINT	function vatom colvar generic opes bias core pytorch
22.009	Glycosylation in calixarenes capsule	chemistry	Metadynamics, glycosylation, supramolecular catalysis	GiovanniMaria Piccini	ANGLE LOWER_WALLS RMSD COORDINATION UPPER_WALLS COMBINE BRIDGE DISTANCES METAD WHOLEMOLECULES FIT_TO_TEMPLATE MATHEVAL FLUSH GROUP UNITS DISTANCE PRINT	function colvar generic multicolvar setup adjmat bias core
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	LOWER_WALLS COORDINATION UPPER_WALLS COORDINATIONNUMBER COMBINE METAD COM FLUSH UNITS GYRATION DISTANCE	function symfunc vatom colvar generic setup bias
21.044	NaCl nucleation	chemistry	metadynamics, DFS clustering	Aaron Finney	FIXEDATOM CLUSTER_DISTRIBUTION INSPHERE Q6 COORDINATIONNUMBER LOCAL_Q6 COMBINE METAD DFSCLUSTERING MFILTER_MORE CLUSTER_NATOMS CONTACT_MATRIX DUMPGRID GROUP HISTOGRAM PRINT	function symfunc vatom generic multicolvar adjmat clusters volumes bias core gridtools
21.033	Multiple-path-metadynamics applied to DNA base-pairing transitions	bio	path-CV, metadynamics, multiple-walker, dna	Alberto Pérez-de-Alba-Ortíz	RESTRAINT CONSTANT UPPER_WALLS COMBINE METAD INCLUDE MOVINGRESTRAINT PRINT	function generic bias
21.030	Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains	bio	parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure	Jim Pfaendtner	TORSION COORDINATION COM METAD INCLUDE ENERGY ALPHABETA GYRATION DISTANCE PBMETAD PRINT	vatom colvar generic multicolvar bias
21.014	how to determine statistically accurate conformational ensembles	bio	metadynamics, metainference, errors, cv, SAXS, ensemble determination	Cristina Paissoni	TORSION ENSEMBLE STATS CENTER CONTACTMAP METAD ANTIBETARMSD SAXS WHOLEMOLECULES BIASVALUE ALPHABETA MOLINFO GYRATION PBMETAD PRINT	secondarystructure function isdb vatom colvar generic multicolvar bias
20.026	Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor	bio	Metadynamics, Umbrella sampling	Brandon Peters	RESTRAINT METAD REWEIGHT_METAD MULTI_RMSD DUMPGRID HISTOGRAM CONVERT_TO_FES PRINT	generic bias gridtools colvar
20.015	Rational design of ASCT2 inhibitors using an integrated experimental-computational approach	bio	ASCT2 transporter, small-molecules, cryo-EM, metainference	Max Bonomi	EMMIVOX LOAD BIASVALUE WHOLEMOLECULES DUMPATOMS GROUP MOLINFO PRINT	isdb generic setup bias core
20.014	amyloid beta small molecule interaction	bio	intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta	Gabriella Heller	TORSION ENSEMBLE COMBINE INCLUDE ENDPLUMED MOLINFO ALPHARMSD COORDINATION ANTIBETARMSD GROUP PBMETAD PRINT DIHCOR PARABETARMSD FLUSH METAINFERENCE GYRATION WHOLEMOLECULES CS2BACKBONE STATS	function secondarystructure isdb colvar generic multicolvar bias core
20.005	Muscarinic M2 receptor/ligand Frequency-Adaptive Metadynamics and QM/MM calculations	bio	Frequency-adaptive metadynamics, multiple-walkers metadynamics, well-tempered metadynamics, GPCR, receptor, Adiabatic Bias MD	Riccardo Capelli	COMBINE ENDPLUMED MOLINFO FUNCPATHMSD CONVERT_TO_FES LOWER_WALLS READ CONTACTMAP COM METAD DUMPGRID HISTOGRAM ABMD PRINT UPPER_WALLS REWEIGHT_METAD FLUSH WHOLEMOLECULES DISTANCE	function vatom colvar generic bias gridtools
20.004	Data-driven collective variables for enhanced sampling	methods	collective variables, machine learning, deep-lda	Luigi Bonati	TORSION OPES_METAD LOWER_WALLS UPPER_WALLS COM LOAD MATHEVAL ENDPLUMED FLUSH PYTORCH_MODEL GROUP UNITS DISTANCE PRINT	function vatom colvar generic setup opes bias core pytorch
19.075	PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python	other	Python, automatic differentiation	Toni Giorgino	RESTRAINT TORSION ANGLE CENTER COMBINE DUMPDERIVATIVES ENDPLUMED CUSTOM GROUP DISTANCE PRINT	function vatom colvar generic bias core
19.074	Asymmetric base pair opening in nucleic acids	bio	double helix, DNA, RNA, unwindability	Giovanni Bussi	RESTRAINT LOWER_WALLS COORDINATION WHOLEMOLECULES ENDPLUMED DISTANCE	generic bias colvar
19.042	Harmonic Linear Discriminant Analysis (HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	UPPER_WALLS COMBINE METAD FLUSH UNITS ENERGY DISTANCE PRINT	function colvar generic setup bias
19.032	Chemical reaction in solution using path collective variables based on coordination patterns	chemistry	chemical reactions, solutions, metadynamics, coordination patterns	Fabio Pietrucci	UPPER_WALLS RESTART METAD DISTANCES PATH FLUSH PRINT	mapping generic setup multicolvar bias
19.028	pRAVE	methods	RAVE, reaction coordinate, deep learning, metadynamics, kinetics	Pratyush Tiwary	TORSION EXTERNAL COMMITTOR COMBINE COM RESTART WHOLEMOLECULES ALPHABETA DISTANCE PRINT	function vatom colvar generic setup multicolvar bias
19.020	PTMetaD-WTE simulation of the Ntail IDP	bio	metadynamics, IDPs, protein folding	Mattia Bernetti	METAD WHOLEMOLECULES ENDPLUMED MOLINFO ENERGY GYRATION ALPHARMSD PRINT	generic bias secondarystructure colvar
19.005	Cmyc small molecule interaction	bio	metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP	Gabriella Heller	GROUP CENTER COORDINATION INCLUDE DISTANCE WHOLEMOLECULES ALPHABETA MOLINFO CS2BACKBONE METAINFERENCE GYRATION PBMETAD PRINT	isdb vatom colvar generic multicolvar bias core
25.008	Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting	methods	metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting	Dhiman Ray	TORSION OPES_METAD ENDPLUMED LOWER_WALLS ENERGY DISTANCE BIASVALUE POSITION UPPER_WALLS CUSTOM RMSD GROUP WHOLEMOLECULES PYTORCH_MODEL PRINT UNITS METAD MOLINFO	function pytorch setup core colvar bias opes generic
25.007	Shaping the glycan landscape. Hidden relationships between linkage and ring distortion induced by carbohydrate-active enzmyes	bio	REST-RECT, REST2, glycan, enzyme, CAZyme, steered	Isabell Grothaus	TORSION MOVINGRESTRAINT DISTANCE RESTRAINT RESTART PUCKERING PRINT METAD MOLINFO	setup colvar bias generic
24.036	Leveraging cryptic ligand envelopes through enhanced molecular simulations	bio	HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope	Francesco Colizzi	TORSION COORDINATION ANGLE DISTANCE HISTOGRAM DUMPGRID CONVERT_TO_FES GROUP WHOLEMOLECULES PRINT	gridtools colvar core generic
24.031	DeepLNE	methods	PATHCV, OPES, OneOPES	Thorben Fröhlking	COORDINATION OPES_EXPANDED ENERGY ERMSD RESTART COMBINE VOLUME ECV_MULTITHERMAL OPES_METAD_EXPLORE PYTORCH_MODEL PRINT MOLINFO	function pytorch setup colvar opes 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 COMMITTOR LOAD GROUP PRINT METAD	setup core colvar bias generic
24.006	Water vapor condensation	chemistry	metadynamics, homogeneous condensation, chemical potential	Shenghui Zhong	CLUSTER_PROPERTIES DFSCLUSTERING CONTACT_MATRIX UNITS COORDINATIONNUMBER UPPER_WALLS METAD CLUSTER_NATOMS PRINT	setup symfunc clusters bias adjmat generic
24.001	A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations	bio	OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis	Dhiman Ray	OPES_METAD TORSION LOWER_WALLS DISTANCE FLUSH COMMITTOR UNITS COMBINE UPPER_WALLS CUSTOM PRINT	function setup colvar bias opes 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	OPES_METAD DISTANCE FIXEDATOM FLUSH UNITS GROUP COORDINATIONNUMBER UPPER_WALLS ZDISTANCES PRINT	setup core symfunc multicolvar colvar vatom bias opes generic
23.027	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, DFS, Q3, Pair Entropy	Aaron Finney	CLUSTER_DISTRIBUTION RESTRAINT HISTOGRAM DFSCLUSTERING LOCAL_AVERAGE DUMPGRID CONTACT_MATRIX DENSITY AROUND LOCAL_Q3 UNITS GROUP COORDINATIONNUMBER LOAD PRINT FIXEDATOM CLUSTER_NATOMS Q3	volumes setup core symfunc gridtools clusters vatom bias adjmat generic
23.025	Probing ion binding to G-quadruplexes and related events	chemistry	metadynamics, repulsive potential, nucleic acids, G-quadruplexes	Marcelo Poleto	DISTANCE RESTART FLUSH DISTANCES FIT_TO_TEMPLATE DUMPATOMS POSITION UNITS COM WHOLEMOLECULES LOWER_WALLS UPPER_WALLS GROUP WRAPAROUND MATHEVAL METAD PRINT	generic function setup core colvar vatom bias multicolvar
23.008	PBMetaD simulations of Histatin5	bio	metadynamics, IDP, Rg, PPII	Francesco Pesce	TORSION GYRATION PBMETAD GROUP WHOLEMOLECULES PRINT MOLINFO	core 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	DISTANCE HISTOGRAM READ REWEIGHT_METAD DUMPGRID CONVERT_TO_FES RMSD MATHEVAL WHOLEMOLECULES PRINT METAD MOLINFO	function gridtools colvar bias generic
23.001	Quantum phase diagram of water	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn-Løland Bore	OPES_EXPANDED ECV_UMBRELLAS_LINE RESTART INCLUDE ENVIRONMENTSIMILARITY LOWER_WALLS UPPER_WALLS PRINT	setup envsim bias opes generic
22.045	Binding mode and mechanism of enzymatic polyethylene terephthalate degradation	bio	metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation	Francesco Colizzi	MOVINGRESTRAINT ANGLE DISTANCE COM WHOLEMOLECULES LOWER_WALLS UPPER_WALLS METAD PRINT	colvar bias generic vatom
22.040	From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure	bio	SARS-CoV-2, Spike, Omicron	Miłosz Wieczór	PCAVARS WHOLEMOLECULES LOWER_WALLS UPPER_WALLS METAD PRINT	mapping bias generic
22.031	Rare Event Kinetics from Adaptive Bias Enhanced Sampling	methods	OPES Flooding, Kinetics, Rate, OPES, Machine Learning	Dhiman Ray	TORSION CONSTANT RMSD WHOLEMOLECULES COMBINE PRINT MOLINFO GROUP POSITION CUSTOM OPES_METAD ENERGY DISTANCE UNITS ENDPLUMED INCLUDE CONTACTMAP COMMITTOR BIASVALUE PYTORCH_MODEL	function pytorch setup core colvar bias opes generic
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	colvar generic
22.021	Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn Løland Bore	OPES_EXPANDED ECV_UMBRELLAS_LINE INCLUDE UPPER_WALLS ENVIRONMENTSIMILARITY LOWER_WALLS PRINT	envsim bias opes generic
22.020	Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA	bio	RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics	Weiwei He	TORSION DISTANCE WHOLEMOLECULES GROUP COM PRINT METAD	core colvar vatom bias generic
22.019	Exploring aspartic protease inhibitor binding to design selective antimalarials	bio	ligand binding, loop opening, path CV, funnel metadynamics, drug development	Raitis Bobrovs	FUNNEL DISTANCE FUNNEL_PS COM WHOLEMOLECULES LOWER_WALLS UPPER_WALLS METAD PATHMSD PRINT	funnel colvar vatom bias generic
22.004	Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques	chemistry	reaction discovery, OPES, collective variables	Umberto Raucci	OPES_METAD COORDINATION LOWER_WALLS DISTANCE LOAD UNITS COM OPES_METAD_EXPLORE PYTORCH_MODEL UPPER_WALLS CUSTOM MATHEVAL GROUP PRINT	pytorch function setup core colvar vatom bias opes generic
21.050	N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity	methods	bio	Isabell Louise Grothaus	PRINT DISTANCE CENTER	colvar vatom generic
21.031	Photo-switchable sulfonulureas in KATP channel	bio	metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels	Katarzyna Walczewska-Szewc	DISTANCE UNITS COM WHOLEMOLECULES LOWER_WALLS UPPER_WALLS METAD PRINT	setup colvar vatom bias generic
21.019	Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations	materials	Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen	Matteo Salvalaglio	DISTANCE MATHEVAL COM TORSIONS PRINT KDE	function multicolvar colvar vatom gridtools generic
21.002	Phase equilibrium of water with hexagonal and cubic ice using the SCAN functional	materials	ice, water, SCAN, OPES, VES, multithermal, crystallization, environment similarity, refcv, reweighting	Pablo Piaggi	VES_LINEAR_EXPANSION BF_LEGENDRE ENERGY TD_UNIFORM Q6 OPES_EXPANDED ECV_UMBRELLAS_LINE RESTART VOLUME OPT_AVERAGED_SGD UPPER_WALLS ENVIRONMENTSIMILARITY ECV_MULTITHERMAL_MULTIBARIC MATHEVAL PRINT	function setup ves symfunc envsim colvar bias opes generic
20.034	Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations	bio	RNA, SARS-CoV-2, partial tempering	Sandro Bottaro	TORSION DISTANCE CENTER ERMSD ABMD RESTART PRINT MOLINFO	setup colvar vatom bias generic
20.027	Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery	bio	SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery	Khaled Abdel-Maksoud	TORSION PRINT METAD DISTANCE	colvar bias generic
20.006	Class B GPCR activation mechanism	bio	metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	LOWER_WALLS ENERGY DISTANCE CENTER RMSD MATHEVAL WHOLEMOLECULES COMBINE UPPER_WALLS METAD MOLINFO PRINT	function colvar vatom bias 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	ENDPLUMED ENERGY DISTANCES GYRATION COORDINATIONNUMBER LOWER_WALLS UPPER_WALLS METAD PRINT	generic symfunc colvar bias multicolvar
19.059	cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide	bio	bias-exchange metadynamics, cis-trans isomerization	Fabrizio Marinelli	RANDOM_EXCHANGES TORSION INCLUDE PRINT METAD	colvar bias generic
19.046	Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding	bio	VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation	Faidon Brotzakis	TORSION LOWER_WALLS ALPHABETA DISTANCE DISTANCES REWEIGHT_METAD BRIDGE RMSD COM WHOLEMOLECULES COMBINE UPPER_WALLS GROUP FUNNEL MOLINFO METAD PRINT	funnel generic function core colvar vatom bias adjmat multicolvar
19.024	PT-MetaD-WTE	methods	metadynamics, WTE, trp cage, PT	Jim Pfaendtner	COORDINATION ENERGY EXTERNAL GROUP METAD	core colvar bias
19.023	RECT	methods	metadynamics, replica exchange	Giovanni Bussi	TORSION GYRATION WHOLEMOLECULES PRINT METAD	colvar bias generic
19.021	Coarse-Grained Directed Simulation	methods	experiment directed simulation, coarse-grain, bias	Glen Hocky	TORSION DISTANCE RESTRAINT COMBINE PRINT EDS	eds function colvar bias generic
19.019	FA-MetaD-JCP-Wang-et-al	bio	Frequency adaptive metadynamics; peptide	Kresten Lindorff-Larsen	ALPHABETA COMMITTOR FLUSH COMBINE PRINT METAD MOLINFO	function bias generic multicolvar
19.014	MIL101(Cr) SBUs assembly	materials	MOFs, nucleation, self-assembly, metadynamics	Matteo Salvalaglio	ENDPLUMED RESTART DISTANCES GYRATION COORDINATIONNUMBER PRINT METAD	generic setup symfunc colvar bias multicolvar
19.012	Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex	Carlo Camilloni	ENDPLUMED DISTANCE RESTRAINT STATS CENTER INCLUDE BIASVALUE UPPER_WALLS RMSD GROUP WHOLEMOLECULES SAXS MOLINFO PRINT	isdb function core colvar vatom bias generic
19.009	RNA tetraloops folding	bio	metadynamics, RNA, folding	Giovanni Bussi	ENDPLUMED ERMSD RMSD WHOLEMOLECULES PRINT METAD MOLINFO	colvar bias generic
19.004	MI Ubiquitin	bio	metainference, NMR	Max Bonomi	METAINFERENCE RDC CS2BACKBONE GROUP WHOLEMOLECULES PRINT MOLINFO	isdb core generic
19.002	EMMI STRA6	bio	metainference, cryo-EM	Max Bonomi	BIASVALUE EMMI GROUP PRINT MOLINFO	core isdb bias generic
25.020	Revealing Water-Mediated Activation Mechanisms in the Beta 1-Adrenergic Receptor via OneOPES-Enhanced Free Energy Landscapes	bio	OneOPES, GPCR, ADRB1, activation, microswitches, conformational changes, allostery	Valerio Rizzi	RMSD ECV_MULTITHERMAL OPES_EXPANDED ENERGY GROUP DISTANCE DISTANCES PATHMSD CENTER PRINT COORDINATION GHOST LOWER_WALLS CUSTOM OPES_METAD_EXPLORE UPPER_WALLS	generic vatom colvar opes bias multicolvar core function
25.013	Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices	bio	umbrella sampling, temperature ramping	Alexander Berlaga	PYTORCH_MODEL DISTANCE GYRATION PRINT RESTRAINT	bias pytorch colvar generic
24.034	Umbrella sampling of ion in transporter SLC26A7	bio	umbrella sampling, transporter, ions	Xiaoli Lu	POSITION PRINT UNITS RESTRAINT	bias colvar generic setup
24.032	DeepLNE++	methods	PATHCV, OPES	Thorben Fröhlking	LOAD TORSION ENERGY GROUP DISTANCE COMBINE PRINT COORDINATION CUSTOM OPES_METAD	generic colvar opes core setup function
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	TORSION CUSTOM DISTANCE MOLINFO COMBINE GYRATION COORDINATION WHOLEMOLECULES PRINT ALPHARMSD OPES_METAD	generic secondarystructure opes colvar function
24.010	Oxytocin metadynamics simulation	bio	metadynamics, oxytocin, peptide	Jan Beránek	METAD TORSION RESTART PRINT FLUSH WHOLEMOLECULES	colvar bias generic setup
23.043	Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling	materials	Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters	Lorenzo Gigli	METAD INCLUDE TRANSPOSE SUM PRINT FLUSH SELECT_COMPONENTS MATHEVAL	generic bias valtools matrixtools function
23.037	Estimating binding free energy of solid binding peptides without extensive sampling	bio	metadynamics, solid binding peptides	Xin Qi	DISTANCE MOLINFO PRINT GYRATION COM LOWER_WALLS PBMETAD UPPER_WALLS	bias colvar generic vatom
23.034	Urea nucleation in water: do long-range forces matter?	materials	LMF theory, Metadynamics, Nucleation	Ziyue Zou	LOAD METAD INCLUDE GROUP CENTER PRINT COORDINATIONNUMBER	generic vatom bias symfunc core setup
23.031	Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN	bio	RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites	Max Bonomi	POSITION METAD FIT_TO_TEMPLATE GROUP WRAPAROUND DISTANCES MOLINFO PRINT CENTER WHOLEMOLECULES SHADOW UPPER_WALLS	generic vatom colvar bias multicolvar isdb core
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	RMSD ENDPLUMED CONTACTMAP OPES_METAD INCLUDE PYTORCH_MODEL COMMITTOR ENERGY ANGLE MOLINFO COMBINE COORDINATION LOWER_WALLS UPPER_WALLS FIT_TO_TEMPLATE GROUP PRINT DISTANCE CENTER WHOLEMOLECULES CUSTOM MATHEVAL FIXEDATOM	generic vatom opes colvar bias core pytorch function
22.042	Metadynamics of NSP10 and variants	bio	metadynamics, NSP10, crystal structure, variants	Shozeb Haider	METAD PRINT TORSION	colvar generic bias
22.039	Driving and characterizing nucleation of urea and glycine polymorphs in water	bio	metadynamics, nucleation, amino acids, polymorphism	Eric Beyerle	LOAD METAD Q6 INCLUDE GROUP CENTER COMBINE COORDINATIONNUMBER PRINT Q4 PAIRENTROPY MATHEVAL	generic vatom gridtools bias symfunc core setup function
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	CONTACTMAP DISTANCE PRINT CENTER	colvar generic vatom
21.049	Multiple-path-metadynamics and PathMaps	methods	path-CV, metadynamics, multiple-walker, multiple paths, pathmap	Alberto Pérez-de-Alba-Ortíz	LOAD METAD TORSION CONSTANT UNITS MOVINGRESTRAINT ENSEMBLE COMBINE PRINT RESTRAINT LOWER_WALLS CUSTOM UPPER_WALLS	generic colvar bias setup function
21.028	From Enhanced Sampling to Reaction Profiles	methods	collective variables, multi-state, machine learning, Deep-TDA	Enrico Trizio	LOAD ENDPLUMED UNITS DISTANCES OPES_METAD PYTORCH_MODEL ANGLE COORDINATION LOWER_WALLS UPPER_WALLS TORSION FIT_TO_TEMPLATE GROUP PRINT DISTANCE CENTER WHOLEMOLECULES MATHEVAL FIXEDATOM	generic vatom opes colvar bias multicolvar core setup pytorch 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	POSITION METAD RESTART PRINT CENTER COORDINATION WHOLEMOLECULES REWEIGHT_BIAS RESTRAINT MATHEVAL	generic vatom colvar bias setup function
20.031	Soft fluorescent nanoshuttles targeting receptors	chemistry	polymers, receptors, nanoparticles, fluorescent probes	Adriana Pietropaolo	PRINT CENTER COORDINATION WHOLEMOLECULES PBMETAD	colvar generic bias vatom
20.030	Converging experimental and computational views of the knotting mechanism of the smallest knotted protein	bio	phi-values, transition state, knotted proteins	Cristina Paissoni	STATS MOLINFO COMBINE PRINT COORDINATION WHOLEMOLECULES RESTRAINT	bias colvar function 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	METAD UNITS PRINT COORDINATION CUSTOM DISTANCES	generic colvar bias multicolvar setup function
19.082	Ammonia Borane Dehydrogenation	chemistry	metadynamics, reaction discovery, hydrogen production, chemistry	Valerio Rizzi	METAD ENDPLUMED GROUP UNITS EXTERNAL RESTART PRINT COMBINE COORDINATIONNUMBER FLUSH	generic bias symfunc core setup function
19.069	Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen	materials	ibuprofen, crystal, solvent, surface	Matteo Salvalaglio	INCLUDE ENDPLUMED GROUP DISTANCE PRINT CENTER	colvar generic core vatom
19.029	WTE-metaD of FF domain of URNF1 C57D variant	bio	metadynamics, mutations, post-translational modification, ff domain	Elena Papaleo	METAD GROUP UPPER_WALLS MOLINFO PRINT GYRATION WHOLEMOLECULES ALPHABETA LOWER_WALLS	generic colvar bias multicolvar core
19.026	Ice Nucleation on Cholesterol Crystals	materials	forward flux sampling, crystal nucleation, water, ice, organic crystals	Gabriele Cesare Sosso	Q6 COMMITTOR CONTACT_MATRIX ENDPLUMED OUTPUT_CLUSTER MFILTER_MORE LOCAL_Q6 DFSCLUSTERING CLUSTER_NATOMS FLUSH CLUSTER_WITHSURFACE	adjmat clusters generic symfunc multicolvar
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 STATS BIASVALUE TORSION ENDPLUMED JCOUPLING RDC ENSEMBLE GYRATION MOLINFO PRINT FLUSH WHOLEMOLECULES PBMETAD CS2BACKBONE	generic colvar bias isdb function
25.024	Sampling glycan-glycan interactions for B22 calculations	bio	B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange	Isabell Louise Grothaus	RESTRAINT METAD PRINT POSITION COM COMBINE DISTANCE	function colvar bias generic vatom
25.015	Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY	materials	Molecular crystal, Force Field, Collective Variable	Pradip Si and Omar Valsson	PRINT TORSIONS SMAC DISTANCES DUMPMULTICOLVAR	symfunc multicolvar generic
25.012	A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis	bio	enzyme catalysis, transition state, structure-activity relationship, free energy surface, reaction mechanism, water, alpha-amylase, sugar, QM/MM MD, OPES, committor function, machine learning	Sudip Das	COORDINATION MATHEVAL PRINT CUSTOM POSITION OPES_METAD COMBINE TORSION INCLUDE LOAD DISTANCE ENERGY FLUSH CELL UNITS BIASVALUE	function colvar bias setup generic opes
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	PRINT CUSTOM ZDISTANCES OPES_METAD FIXEDATOM DISTANCES DISTANCE GROUP UPPER_WALLS FLUSH UNITS COMMITTOR COORDINATIONNUMBER	function symfunc colvar multicolvar core bias setup generic vatom opes
25.003	Surrogate Model CV	methods	Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding	Sompriya Chatterjee	WHOLEMOLECULES PYTORCH_MODEL PRINT CUSTOM OPES_METAD COMBINE MOLINFO TORSION COMMITTOR DISTANCE ENERGY GROUP ENDPLUMED MATHEVAL	function pytorch colvar core generic opes
25.002	M3_PCV-ABMD	chemistry	Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor	Gian Marco Elisi	PRINT PATHMSD ABMD ENDPLUMED UNITS UPPER_WALLS	bias colvar setup generic
25.001	RNA G-quadruplex folding with ST-metaD protocol	bio	RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD	Pavlína Pokorná	WHOLEMOLECULES METAD COMBINE MOLINFO ERMSD	bias function colvar 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	COORDINATION PRINT CUSTOM OPES_METAD FIXEDATOM TORSION LOWER_WALLS RESTART DISTANCE FIT_TO_TEMPLATE GROUP PATH PYTORCH_MODEL CENTER WHOLEMOLECULES UPPER_WALLS	function pytorch colvar mapping core bias setup generic vatom opes
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	CUSTOM FIXEDATOM TORSION DISTANCE GROUP WHOLEMOLECULES COMMITTOR UPPER_WALLS COORDINATION FIT_TO_TEMPLATE CENTER CONTACTMAP MATHEVAL RMSD METAD OPES_METAD MOLINFO ANGLE PRINT COMBINE ENDPLUMED	function colvar core bias generic vatom opes
23.045	Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state	bio	Path CVs Metadynamics, GPCRs activation transition	Vittorio Limongelli	ALPHARMSD PRINT METAD MOLINFO PATHMSD LOWER_WALLS INCLUDE DISTANCE FUNCPATHMSD UPPER_WALLS CONTACTMAP	function colvar bias generic secondarystructure
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	WRAPAROUND RMSD PRINT MOLINFO CENTER STATS SAXS DISTANCE GROUP UPPER_WALLS ENSEMBLE BIASVALUE	function isdb colvar core bias generic vatom
23.019	Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors	bio	binding pathway, binding energy, sketch-map, drug development	Raitis Bobrovs	METAD PRINT CUSTOM COM COLLECT_FRAMES PATHMSD DISSIMILARITIES LANDMARK_SELECT_FPS TRANSPOSE DISTANCE VORONOI UPPER_WALLS SKETCHMAP_PROJECTION SKETCHMAP VSTACK WHOLEMOLECULES	function valtools matrixtools colvar dimred bias generic vatom landmarks
23.003	Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations	methods	metadynamics, alchemical variable, alchemical free energy calculations	Wei-Tse Hsu	READ METAD PRINT TORSION EXTRACV	bias colvar generic
22.013	Ligand dissociation from PreQ1 riboswitch	bio	ligand, RNA, metadynamics, pRAVE	Yihang Wang	RMSD METAD PRINT COM COMBINE MOLINFO COMMITTOR DISTANCE WHOLEMOLECULES COORDINATIONNUMBER	function symfunc colvar bias generic vatom
22.005	Collective Variable for Metadynamics Derived from AlphaFold Output	bio	AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable	Vojtech Spiwok	LOAD METAD WHOLEMOLECULES PRINT	bias setup generic
21.047	Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations	materials	pair entropy, metadynamics, ves, solids, crystallization	Pablo Piaggi	PAIRENTROPY METAD PRINT COMBINE VOLUME RESTART LOAD ENERGY TD_WELLTEMPERED BF_LEGENDRE OPT_AVERAGED_SGD VES_LINEAR_EXPANSION	function gridtools colvar bias setup ves generic
21.032	Metal-coupled folding mechanism to metallothionein	bio	parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination	Manuel-Peris Diaz	COORDINATION GROUP PBMETAD UNITS WHOLEMOLECULES	colvar core bias setup generic
21.023	Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling	methods	enhanced sampling, collective variables, machine learning	Jakub Rydzewski	METAD PRINT CUSTOM TORSION INCLUDE DISTANCE ENERGY CONSTANT UNITS REWEIGHT_METAD BIASVALUE	function colvar bias setup generic
21.009	Nucleation rates from small scale atomistic simulations and transition state theory	materials	kinetics, free energy barriers, nucleation, droplets, metadynamics	Kristof Bal	METAD PRINT MOVINGRESTRAINT HISTOGRAM LOAD CONVERT_TO_FES DUMPGRID UPPER_WALLS FLUSH UNITS REWEIGHT_METAD COMMITTOR COORDINATIONNUMBER	symfunc gridtools bias setup generic
21.004	Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy	bio	machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding	Dorothea Gobbo	METAD PRINT PATHMSD LOWER_WALLS RESTART UPPER_WALLS WHOLEMOLECULES	bias colvar setup generic
20.024	Gaussian Mixture Based Enhanced Sampling (GAMBES)	methods	enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias	Jayashrita Debnath	PRINT COMBINE LOWER_WALLS TORSION LOAD DISTANCE ENERGY GROUP DISTANCES UPPER_WALLS UNITS	function colvar multicolvar core bias setup generic
20.023	metadynminer and metadynminer3d	methods	metadynamics, visualization, R	Vojtech Spiwok	METAD PRINT TORSION	bias colvar generic
20.018	Free energy barriers from biased molecular dynamics simulations	methods	kinetics, free energy barriers, chemical reactions, nucleation, metadynamics	Kristof Bal	LOWER_WALLS HISTOGRAM DISTANCE DENSITY FLUSH REWEIGHT_METAD COORDINATIONNUMBER COORDINATION REWEIGHT_BIAS LOAD CONVERT_TO_FES SPRINT CENTER UNITS Q6 METAD LOCAL_AVERAGE DUMPGRID ENERGY PAIRENTROPY PRINT COMBINE VOLUME CONTACT_MATRIX UPPER_WALLS	function symfunc gridtools colvar bias setup generic volumes vatom adjmat sprint
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_DUMMY PRINT VOLUME RESTART TD_WELLTEMPERED ENVIRONMENTSIMILARITY BF_LEGENDRE OPT_AVERAGED_SGD Q6 MATHEVAL VES_LINEAR_EXPANSION UPPER_WALLS	envsim function symfunc colvar bias setup ves generic
19.083	Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis	chemistry	metadynamics, chemical reactions, reaction discovery	Valerio Rizzi	METAD PRINT COMBINE RESTART DISTANCES GROUP ENDPLUMED FLUSH UNITS COORDINATIONNUMBER UPPER_WALLS	function symfunc multicolvar core bias setup generic
19.077	Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	METAD PRINT COM GYRATION MOLINFO DISTANCE ENERGY UPPER_WALLS	bias colvar generic vatom
19.065	Molecular Enhanced Sampling with Autoencoders	methods	enhanced sampling, collective variables, deep learning	Wei Chen	RESTRAINT POSITION COM COMBINE ANN	function colvar bias annfunc vatom
19.049	Determining the sizes of solid/liquid clusters in MD trajectories of nucleation	methods	nucleation, metadynamics, clustering, Steinhardt order parameters	Gareth Tribello	DFSCLUSTERING COORDINATIONNUMBER METAD PRINT CUSTOM SMAC OUTER_PRODUCT CLUSTER_NATOMS MATRIX_VECTOR_PRODUCT CONTACT_MATRIX CLUSTER_PROPERTIES DISTANCES MORE_THAN CLUSTER_DISTRIBUTION Q6 ONES LOCAL_Q6 OUTPUT_CLUSTER	function clusters symfunc matrixtools multicolvar bias generic adjmat
19.018	Excited state FEP/Metadynamics simulations	chemistry	metadynamics, FEP, excited states, conjugated polymers, torsional potential	Adriana Pietropaolo	MATHEVAL METAD PRINT TORSION CONSTANT WHOLEMOLECULES BIASVALUE	bias function colvar generic
25.026	Deciphering the Molecular Mechanisms of Startle Disease - the Role of the Asn46Lys Mutation in the Glycine Receptor	bio	metadynamics, glycine receptors, funnel metadynamics	Jacob Adam Clark	FUNNEL COM FUNNEL_PS PRINT METAD LOWER_WALLS UPPER_WALLS	funnel vatom bias generic
25.017	Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity	bio	EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase	Samuel Hoff	MOLINFO BIASVALUE WHOLEMOLECULES GROUP PRINT EMMIVOX	core bias isdb generic
24.023	Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21. A Machine-Learning-Aided Enhanced Sampling Study	bio	RNA, miRNA, OneOPES, ligand binding, conformational changes	Valerio Rizzi	DISTANCE CUSTOM COORDINATION GROUP PRINT RESTART OPES_EXPANDED ENERGY OPES_METAD_EXPLORE ECV_MULTITHERMAL COMBINE TORSION	setup colvar core opes function generic
24.016	Cryo-EM guided simulations of ribozyme	bio	metainference, cryo-EM	Giovanni Bussi	INCLUDE MOLINFO ERMSD BIASVALUE WHOLEMOLECULES GROUP RESTRAINT PRINT EMMIVOX	bias colvar core isdb generic
24.004	Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables	materials	metadynamics, nucleation, machine learning	Ziyue Zou	INCLUDE LOAD GROUP PRINT METAD RESTART	core bias setup generic
23.038	Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor	bio	protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics	Timothy Clark	DISTANCE MOLINFO WHOLEMOLECULES RMSD PRINT METAD MATHEVAL	bias function colvar generic
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	DISTANCE CUSTOM COORDINATION PYTORCH_MODEL WHOLEMOLECULES UNITS GROUP PATH FIT_TO_TEMPLATE CENTER PRINT OPES_METAD OPES_METAD_EXPLORE FIXEDATOM TORSION LOWER_WALLS UPPER_WALLS	vatom bias setup mapping colvar core opes pytorch function generic
23.012	JAK2 2D meta-eABF PMF with statistical analysis	bio	2D meta-eABF, path CV, PMF	Istvan Kolossvary	CUSTOM BIASVALUE FLUSH PRINT METAD DRR PATHMSD LOWER_WALLS UPPER_WALLS	bias generic colvar function drr
23.007	Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains	bio	metadynamics, peptoids, parallel-bias metadynamics	Jim Pfaendtner	INCLUDE COM WHOLEMOLECULES COORDINATION RESTRAINT PBMETAD GYRATION PRINT TORSION	vatom colvar bias generic
22.044	Colloid Crystallisation Analyses	materials	Q4, Q6, Pair Entropy, DFS	Aaron Finney	LOCAL_Q4 Q4 CLUSTER_NATOMS GROUP LOCAL_Q6 COORDINATIONNUMBER PRINT LOCAL_AVERAGE MFILTER_MORE COMBINE Q6 MFILTER_LESS CONTACT_MATRIX DFSCLUSTERING	adjmat core clusters multicolvar symfunc function generic
22.043	Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES	bio	OPES, RNA, Tetraloop, Folding	Gül Zerze	WHOLEMOLECULES ECV_UMBRELLAS_LINE PRINT ENERGY OPES_EXPANDED ECV_MULTITHERMAL CONTACTMAP	opes colvar generic
22.038	Enhanced Sampling Aided Design of Molecular Photoswitches	chemistry	reaction discovery, OPES explore, graph CV	Umberto Raucci	CUSTOM COORDINATION PYTORCH_MODEL UNITS PRINT OPES_METAD_EXPLORE	setup colvar opes pytorch function generic
22.028	N-glycan conformer distributions in atomistic simulation	bio	REST2, RECT, N-glycan, pucker	Isabell Grothaus	PUCKERING MOLINFO HISTOGRAM READ DUMPGRID CONVERT_TO_FES PRINT METAD TORSION	bias colvar gridtools generic
22.025	Bubble nucleation rate predictions in a Lennard-Jones fluid	materials	free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation	Kristof Bal	VOLUME LOAD HISTOGRAM CUSTOM BIASVALUE RESTRAINT UNITS DUMPGRID CONVERT_TO_FES FLUSH COORDINATIONNUMBER REWEIGHT_BIAS PRINT MOVINGRESTRAINT COMMITTOR ANN UPPER_WALLS	bias setup colvar annfunc symfunc function gridtools generic
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	DISTANCE MOLINFO COORDINATION WHOLEMOLECULES ANGLE FLUSH ALPHARMSD PRINT METAD ALPHABETA TORSION UPPER_WALLS	bias colvar secondarystructure multicolvar generic
22.006	Peptide framework for screening the effects of amino acids on assembly	bio	metadynamics, peptides	Andrew White	INCLUDE COM HISTOGRAM GROUP DUMPGRID GYRATION CONVERT_TO_FES REWEIGHT_BIAS PRINT DISTANCES METAD COMBINE	vatom bias colvar core multicolvar function gridtools generic
22.002	GAMBES_SAMPL5_RATES	other	GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding	Jayashrita Debnath	LOAD DISTANCE PYTORCH_MODEL COORDINATION WHOLEMOLECULES GROUP ANGLE FIT_TO_TEMPLATE CENTER FLUSH PRINT COMMITTOR MATHEVAL ENERGY ENDPLUMED FIXEDATOM UPPER_WALLS	vatom bias setup colvar core pytorch function 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	DISTANCE COM CUSTOM UNITS PRINT METAD TORSION LOWER_WALLS UPPER_WALLS	vatom bias setup colvar function generic
21.043	Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes	chemistry	well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability	Huixia Lu	FIT_TO_TEMPLATE PRINT METAD FIXEDATOM TORSION	bias vatom colvar generic
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 COM BIASVALUE WHOLEMOLECULES GROUP PRINT RESTART EMMI UPPER_WALLS	vatom bias setup colvar core isdb generic
21.026	Probing allosteric regulations with coevolution-driven molecular simulations	bio	metadynamics, coevolution, allostery, adenylate cyclase	Francesco Colizzi	DISTANCE COM WHOLEMOLECULES UNITS PRINT METAD PATHMSD UPPER_WALLS	vatom bias setup colvar generic
21.017	All-atom simulations of the Vav1 AD construct	bio	metadynamics, parallel-bias, well-tempered	Simone Orioli	MOLINFO WHOLEMOLECULES PBMETAD GROUP ALPHARMSD REWEIGHT_BIAS RESTART PRINT METAD ALPHABETA CONTACTMAP	bias setup colvar secondarystructure core multicolvar generic
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
21.008	Multi-replica biased sampling for photoisomerization processes in conjugated polymers	methods	metadynamics, FEP, replica-exchange	Adriana Pietropaolo	BIASVALUE WHOLEMOLECULES PBMETAD CONSTANT PRINT RESTART MATHEVAL TORSION	bias setup colvar function generic
21.005	Crystallization Collective Variable	methods	Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA	Tarak Karmakar	LOAD PYTORCH_MODEL GROUP FLUSH PRINT OPES_METAD MATHEVAL LOWER_WALLS UPPER_WALLS	bias setup core opes pytorch function generic
20.016	Predicting polymorphism in molecular crystals using orientational entropy	materials	metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy	Pablo Piaggi	INCLUDE VOLUME LOAD GROUP CENTER PRINT METAD UPPER_WALLS	vatom bias setup colvar core 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	UNITS GYRATION MOVINGRESTRAINT PRINT ENDPLUMED	bias setup colvar generic
19.058	Constrained MD for maintaining a cavity in a calculation	chemistry	constrained MD, porous molecules, porosity, cavity	Kim Jelfs	COM FLUSH MOVINGRESTRAINT PRINT DISTANCES RESTART INPLANEDISTANCES	vatom bias setup multicolvar generic
19.056	maze	methods	maze, ligand unbinding	Jakub Rydzewski	MAZE_SIMULATED_ANNEALING UNITS MAZE_LOSS POSITION PRINT MAZE_OPTIMIZER_BIAS	maze setup colvar generic
19.053	Capillary fluctuations with PLUMED	methods	nucleation, surface tension, capillary fluctuations	Gareth Tribello	FOURIER_TRANSFORM FCCUBIC GROUP UNITS DUMPGRID CENTER FIND_CONTOUR_SURFACE MORE_THAN MULTICOLVARDENS	vatom setup contour core symfunc function gridtools fourier
19.051	Solid liquid interfacial free energy out of equilibrium	materials	metadynamics, nucleation, surface excess free energy	Gareth Tribello	FCCUBIC CELL UNITS PRINT METAD ENDPLUMED AROUND LOWER_WALLS UPPER_WALLS	bias volumes setup colvar symfunc generic
19.031	Ice nucleation using PIV-based path coordinates	materials	phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics	Silvio Pipolo	CELL PRINT METAD FUNCPATHMSD PIV LOWER_WALLS UPPER_WALLS	piv bias colvar function generic
19.013	RNA FF FITTING	methods	force field, RNA	Giovanni Bussi	INCLUDE PUCKERING MOLINFO BIASVALUE CONSTANT MATHEVAL TORSION	bias function colvar generic
19.007	EMMI Microtubules	bio	metainference, cryo-EM	Max Bonomi	MOLINFO BIASVALUE WHOLEMOLECULES GROUP PRINT EMMI	core bias isdb generic

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