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
25.015	Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY	materials	Molecular crystal, Force Field, Collective Variable	Pradip Si and Omar Valsson	DISTANCES TORSIONS SMAC PRINT DUMPMULTICOLVAR	multicolvar generic symfunc
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	GROUP DISTANCE RESTART UNITS UPPER_WALLS PRINT COORDINATION CUSTOM OPES_METAD LOWER_WALLS COMMITTOR	colvar bias opes function core generic setup
24.024	Host-Guest binding free energies à la carte, an automated OneOPES protocol	bio	OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest	Valerio Rizzi	GROUP DISTANCE WHOLEMOLECULES UPPER_WALLS ANGLE TORSION FIT_TO_TEMPLATE PRINT ECV_MULTITHERMAL OPES_EXPANDED FIXEDATOM MATHEVAL COORDINATION ENERGY CENTER LOWER_WALLS OPES_METAD_EXPLORE ENDPLUMED	colvar bias opes function vatom core generic
24.016	Cryo-EM guided simulations of ribozyme	bio	metainference, cryo-EM	Giovanni Bussi	GROUP RESTRAINT EMMIVOX WHOLEMOLECULES BIASVALUE ERMSD PRINT MOLINFO INCLUDE	colvar bias isdb core generic
23.044	Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition	materials	metadynamics, interlocked molecules	Luigi Leanza	GROUP DUMPGRID PRINT HISTOGRAM COORDINATION READ METAD COMMITTOR CONVERT_TO_FES ENDPLUMED	colvar gridtools bias core generic
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	SELECT_COMPONENTS TRANSPOSE SUM PRINT MATHEVAL INCLUDE METAD FLUSH	bias function valtools generic matrixtools
23.034	Urea nucleation in water: do long-range forces matter?	materials	LMF theory, Metadynamics, Nucleation	Ziyue Zou	GROUP COORDINATIONNUMBER PRINT LOAD INCLUDE CENTER METAD	bias symfunc vatom core generic setup
23.028	Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process	chemistry	Ammonia decomposition; Dynamics;OPES; Neural Network potential	Manyi Yang	GROUP COORDINATIONNUMBER DISTANCE ZDISTANCES DISTANCES COM UNITS UPPER_WALLS PRINT FIXEDATOM MATHEVAL ENERGY OPES_METAD CUSTOM COMMITTOR LOWER_WALLS FLUSH	multicolvar colvar bias opes symfunc function vatom core generic setup
23.011	OneOPES, a combined enhanced sampling method to rule them all	bio	OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding	Valerio Rizzi	DISTANCE TORSION PRINT ECV_MULTITHERMAL OPES_EXPANDED MOLINFO ENERGY METAD OPES_METAD_EXPLORE ENDPLUMED	opes generic colvar bias
23.010	An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands	bio	GPCR, binding free energy, free energy surface	Timothy Clark	DISTANCE BIASVALUE UPPER_WALLS WHOLEMOLECULES PRINT MATHEVAL LOWER_WALLS METAD CONSTANT	generic colvar function bias
23.004	Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point	chemistry	water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential	Pablo Piaggi	ECV_UMBRELLAS_LINE DUMPGRID RESTART UPPER_WALLS PRINT HISTOGRAM LOWER_WALLS ENVIRONMENTSIMILARITY OPES_EXPANDED	gridtools bias opes envsim generic setup
23.000	Atomistic simulations of RNA tetraloop folding via PTWTE-WTM	bio	parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding	Gül Zerze	WHOLEMOLECULES UPPER_WALLS CONTACTMAP PRINT ENERGY LOWER_WALLS METAD	generic colvar bias
22.027	Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain	Max Bonomi	RMSD PRINT	generic colvar
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	GROUP EMMI RESTART COM UPPER_WALLS WHOLEMOLECULES TORSION RMSD PBMETAD PRINT BIASVALUE MOLINFO COORDINATION	colvar bias isdb vatom core generic setup
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	DISTANCE BF_WAVELETS TD_UNIFORM POSITION BF_CHEBYSHEV INCLUDE BF_CUBIC_B_SPLINES VES_OUTPUT_BASISFUNCTIONS VES_LINEAR_EXPANSION UNITS UPPER_WALLS PRINT BF_LEGENDRE ENERGY OPT_AVERAGED_SGD COORDINATION METAD OPT_ADAM BF_GAUSSIANS TD_WELLTEMPERED FLUSH	colvar bias ves generic setup
22.000	Amyloid precursor protein processing by human γ-secretase	bio	Bias Exchange Metadynamics, Helix unfolding, coupled binding	Xiaoli Lu	DISTANCE UNITS CONTACTMAP PRINT ANTIBETARMSD INCLUDE MOLINFO COORDINATION ALPHARMSD CENTER METAD RANDOM_EXCHANGES	colvar bias secondarystructure vatom generic setup
21.032	Metal-coupled folding mechanism to metallothionein	bio	parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination	Manuel-Peris Diaz	GROUP UNITS PBMETAD WHOLEMOLECULES COORDINATION	colvar bias core generic setup
21.027	EGFR activating mutations mechanism	bio	metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA	Francesco Gervasio	DISTANCE WHOLEMOLECULES UPPER_WALLS CONTACTMAP PRINT MATHEVAL MOLINFO INCLUDE ENERGY ALPHARMSD LOWER_WALLS METAD	colvar bias secondarystructure function generic
21.022	Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly	materials	parallel bias metadynamics, adsorption, peptide	Xin Qi	DISTANCE COM UPPER_WALLS PBMETAD PRINT GYRATION MOLINFO ENERGY LOWER_WALLS	vatom generic colvar bias
21.003	aSYN SAXS metainference	bio	metainference, SAXS	Kresten Lindorff-Larsen	GROUP METAINFERENCE WHOLEMOLECULES PBMETAD BIASVALUE PRINT EEFSOLV GYRATION SAXS MOLINFO ALPHARMSD CENTER FLUSH	colvar bias secondarystructure isdb vatom core generic
20.021	Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins.	bio	phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution	Cristina Paissoni	RESTRAINT STATS WHOLEMOLECULES PRINT MOLINFO COORDINATION	generic colvar function bias
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	GROUP WHOLEMOLECULES INCLUDE ALPHARMSD PARABETARMSD STATS COMBINE CS2BACKBONE ENSEMBLE METAINFERENCE PRINT ANTIBETARMSD COORDINATION DIHCOR PBMETAD TORSION GYRATION MOLINFO FLUSH ENDPLUMED	multicolvar colvar bias secondarystructure function isdb core 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	DISTANCES UNITS PRINT COORDINATION CUSTOM METAD	multicolvar colvar bias function generic setup
19.073	On the role of enthalpic and entropic contributions on the conformational free energy landscape of MIL-101(Cr) building units	materials	metadynamics, MOF, MIL101Cr, conformational	Matteo Salvalaglio	COORDINATIONNUMBER DISTANCES UPPER_WALLS PRINT GYRATION ENERGY LOWER_WALLS METAD ENDPLUMED	multicolvar colvar bias symfunc generic
19.052	Gibbs free energy of homogeneous nucleation	materials	nucleation, surface excess free energy	Gareth Tribello	UNITS UPPER_WALLS PRINT CELL FCCUBIC METAD ENDPLUMED	colvar bias symfunc generic setup
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	DISTANCE COM UPPER_WALLS PRINT ENERGY METAD	vatom generic colvar bias
19.037	Scission free energy of organic dyes	chemistry	metadynamics, multiple walkers, matheval/lepton	Paolo Raiteri	DISTANCE RESTART UNITS UPPER_WALLS PRINT MATHEVAL METAD FLUSH	colvar bias function generic setup
19.021	Coarse-Grained Directed Simulation	methods	experiment directed simulation, coarse-grain, bias	Glen Hocky	DISTANCE RESTRAINT TORSION PRINT COMBINE EDS	colvar eds bias function generic
19.013	RNA FF FITTING	methods	force field, RNA	Giovanni Bussi	BIASVALUE PUCKERING TORSION MATHEVAL INCLUDE MOLINFO CONSTANT	generic colvar function bias
19.011	Automatic Gradient Computation for Collective Variables	other	gradient, differentiation, curvature	Toni Giorgino	ENDPLUMED	generic
19.007	EMMI Microtubules	bio	metainference, cryo-EM	Max Bonomi	GROUP EMMI WHOLEMOLECULES BIASVALUE PRINT MOLINFO	core generic isdb bias
19.002	EMMI STRA6	bio	metainference, cryo-EM	Max Bonomi	GROUP EMMI BIASVALUE PRINT MOLINFO	core generic isdb bias
19.001	RNA SHAPE	bio	metadynamics, RNA, ligand binding	Giovanni Bussi	DISTANCE DISTANCES UPPER_WALLS ANGLE ERMSD PRINT COMBINE MOLINFO INCLUDE LOWER_WALLS METAD FLUSH RANDOM_EXCHANGES	multicolvar colvar bias function 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	WHOLEMOLECULES WRAPAROUND CENTER RMSD UPPER_WALLS LOWER_WALLS GROUP PRINT CUSTOM METAD MATHEVAL COM FUNNEL_PS FUNNEL TORSION COORDINATION COMMITTOR OPES_METAD	vatom core opes funnel bias function colvar generic
24.034	Umbrella sampling of ion in transporter SLC26A7	bio	umbrella sampling, transporter, ions	Xiaoli Lu	RESTRAINT POSITION PRINT UNITS	colvar setup bias 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	PRINT OPES_EXPANDED GROUP COMBINE CUSTOM TORSION RESTART OPES_METAD_EXPLORE ENERGY ECV_MULTITHERMAL COORDINATION DISTANCE	core opes setup function colvar generic
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	PRINT UPPER_WALLS ENERGY COORDINATION DISTANCE OPES_METAD	opes colvar bias generic
24.012	Molecular simulations to investigate the impact of N6-methylation in RNA recognition	bio	metadynamics, alchemistry, RNA modification, RNA:protein interactions	Giovanni Bussi	PRINT CENTER UPPER_WALLS LOWER_WALLS GROUP COMBINE MOLINFO GHBFIX METAD COM DEBUG COORDINATION DISTANCE BIASVALUE	vatom core bias function colvar generic
24.010	Oxytocin metadynamics simulation	bio	metadynamics, oxytocin, peptide	Jan Beránek	WHOLEMOLECULES PRINT METAD RESTART TORSION FLUSH	colvar setup bias generic
23.031	Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN	bio	RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites	Max Bonomi	WHOLEMOLECULES SHADOW WRAPAROUND PRINT UPPER_WALLS CENTER POSITION GROUP MOLINFO METAD FIT_TO_TEMPLATE DISTANCES	vatom core isdb multicolvar bias colvar generic
23.027	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, DFS, Q3, Pair Entropy	Aaron Finney	DENSITY LOAD HISTOGRAM Q3 LOCAL_AVERAGE CLUSTER_NATOMS LOCAL_Q3 CONTACT_MATRIX GROUP PRINT DFSCLUSTERING COORDINATIONNUMBER RESTRAINT FIXEDATOM UNITS CLUSTER_DISTRIBUTION AROUND DUMPGRID	vatom core clusters gridtools symfunc setup adjmat bias volumes generic
23.026	Machine Learning Nucleation Collective Variables with Graph Neural Networks	chemistry	Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks	Florian Dietrich	Q6 PRINT MOVINGRESTRAINT LOWER_WALLS GROUP COMBINE LOCAL_Q6 METAD MFILTER_MORE COORDINATIONNUMBER	core symfunc multicolvar bias function generic
23.023	Rational design of novel biomimetic sequence-defined polymers for mineralization applications	methods	metadynamics, surface binding, biomimetic mineralization	Kaylyn Torkelson	PRINT UPPER_WALLS GYRATION COM COORDINATION DISTANCE PBMETAD	vatom colvar bias generic
23.019	Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors	bio	binding pathway, binding energy, sketch-map, drug development	Raitis Bobrovs	WHOLEMOLECULES PRINT UPPER_WALLS PATHMSD CUSTOM VORONOI METAD LANDMARK_SELECT_FPS COM COLLECT_FRAMES VSTACK DISSIMILARITIES TRANSPOSE DISTANCE SKETCHMAP_PROJECTION SKETCHMAP	vatom matrixtools landmarks dimred bias function colvar valtools generic
23.013	Path meta-eABF simulation of large scale conformational change in STING protein	methods	meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint	Istvan Kolossvary	PRINT UPPER_WALLS LOWER_WALLS PATHMSD CUSTOM TIME METAD UNITS DRR BIASVALUE FLUSH	drr setup bias function colvar generic
23.012	JAK2 2D meta-eABF PMF with statistical analysis	bio	2D meta-eABF, path CV, PMF	Istvan Kolossvary	PRINT UPPER_WALLS LOWER_WALLS PATHMSD CUSTOM METAD DRR BIASVALUE FLUSH	generic bias function colvar drr
23.001	Quantum phase diagram of water	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn-Løland Bore	PRINT UPPER_WALLS OPES_EXPANDED LOWER_WALLS ENVIRONMENTSIMILARITY RESTART INCLUDE ECV_UMBRELLAS_LINE	opes setup envsim bias generic
22.045	Binding mode and mechanism of enzymatic polyethylene terephthalate degradation	bio	metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation	Francesco Colizzi	WHOLEMOLECULES PRINT UPPER_WALLS MOVINGRESTRAINT LOWER_WALLS ANGLE METAD COM DISTANCE	vatom colvar bias generic
22.032	Reciprocal barrier restraint. Application to path-meta-eABF	methods	restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC	Istvan Kolossvary	PRINT PATHMSD CUSTOM METAD DRR BIASVALUE FLUSH	generic bias function colvar drr
22.028	N-glycan conformer distributions in atomistic simulation	bio	REST2, RECT, N-glycan, pucker	Isabell Grothaus	HISTOGRAM PUCKERING PRINT CONVERT_TO_FES READ MOLINFO METAD TORSION DUMPGRID	colvar generic bias gridtools
22.026	Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification	materials	Peptoid, silica	Jim Pfaendtner	PRINT UPPER_WALLS MOLINFO GYRATION COM DISTANCE PBMETAD	vatom colvar bias generic
22.013	Ligand dissociation from PreQ1 riboswitch	bio	ligand, RNA, metadynamics, pRAVE	Yihang Wang	WHOLEMOLECULES PRINT RMSD COORDINATIONNUMBER MOLINFO COMBINE METAD COM COMMITTOR DISTANCE	vatom symfunc bias function colvar generic
22.011	Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck	methods	metadynamics, membrane permeation, protein folding	Shams Mehdi	WHOLEMOLECULES XANGLES PRINT UPPER_WALLS ZANGLES LOWER_WALLS MOLINFO CUSTOM COMBINE METAD MATHEVAL COM YANGLES TORSION DISTANCE ALPHABETA	vatom multicolvar bias function colvar generic
22.002	GAMBES_SAMPL5_RATES	other	GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding	Jayashrita Debnath	LOAD ENDPLUMED WHOLEMOLECULES UPPER_WALLS CENTER PRINT GROUP ANGLE PYTORCH_MODEL FIT_TO_TEMPLATE MATHEVAL FIXEDATOM ENERGY COORDINATION COMMITTOR DISTANCE FLUSH	vatom core setup bias function colvar pytorch generic
21.038	Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics	materials	metadynamics, SGOOP, nucleation, urea	Ziyue Zou	LOAD PRINT CENTER GROUP COMBINE METAD INCLUDE ENERGY COORDINATIONNUMBER VOLUME	vatom core symfunc setup bias function colvar generic
21.035	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, interface	Aaron Finney	LOAD PRINT GROUP RESTRAINT FIXEDATOM DISTANCE	vatom core setup bias colvar 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	Q6 VES_LINEAR_EXPANSION PRINT OPES_EXPANDED UPPER_WALLS ENVIRONMENTSIMILARITY OPT_AVERAGED_SGD ECV_MULTITHERMAL_MULTIBARIC MATHEVAL RESTART ENERGY BF_LEGENDRE ECV_UMBRELLAS_LINE TD_UNIFORM VOLUME	symfunc opes setup bias envsim function colvar ves generic
20.033	COVID-19 Spike protein opening transition mechanism	bio	EMMI, CryoEM, COVID-19, Spike, Metainference	Faidon Brotzakis	WHOLEMOLECULES DISTANCES HISTOGRAM PRINT RMSD CONVERT_TO_FES EMMI READ GROUP MOLINFO BIASVALUE DUMPGRID	core isdb gridtools multicolvar bias colvar generic
20.026	Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor	bio	Metadynamics, Umbrella sampling	Brandon Peters	MULTI_RMSD HISTOGRAM PRINT CONVERT_TO_FES REWEIGHT_METAD METAD RESTRAINT DUMPGRID	colvar generic bias gridtools
20.025	The role of water in host-guest interaction	bio	ligand binding, water, opes, SAMPL5	Valerio Rizzi	WHOLEMOLECULES ENDPLUMED PRINT CENTER UPPER_WALLS GROUP ANGLE PYTORCH_MODEL FIT_TO_TEMPLATE MATHEVAL FIXEDATOM ENERGY COORDINATION DISTANCE OPES_METAD	vatom core opes bias function colvar pytorch generic
20.019	Systematic finite-temperature reduction of crystal energy landscapes	materials	crystals, organics, structure prediction	Matteo Salvalaglio	PRINT UPPER_WALLS LOWER_WALLS METAD MATHEVAL CELL ENERGY VOLUME	function colvar bias generic
20.010	Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations	materials	water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling	Pablo Piaggi	Q6 OPT_DUMMY VES_LINEAR_EXPANSION PRINT UPPER_WALLS ENVIRONMENTSIMILARITY OPT_AVERAGED_SGD TD_WELLTEMPERED RESTART MATHEVAL BF_LEGENDRE VOLUME	symfunc setup envsim bias function colvar ves generic
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	WHOLEMOLECULES PRINT UPPER_WALLS GROUP MOLINFO PATHMSD METAD RESTART	core setup bias colvar generic
19.077	Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	PRINT UPPER_WALLS MOLINFO METAD GYRATION COM ENERGY DISTANCE	vatom colvar bias generic
19.072	SINE hairpin MD+NMR	bio	metadynamics, RNA, NMR	Giovanni Bussi	WHOLEMOLECULES PRINT MOLINFO METAD SORT COM MATHEVAL INCLUDE TORSION MAXENT COORDINATION DISTANCE FLUSH	vatom bias function colvar generic
19.070	Unexpected Dynamics in the UUCG RNA Tetraloop	bio	well-tempered metadynamics, RNA, UUCG, maximum entropy	Sandro Bottaro	WHOLEMOLECULES PRINT RMSD MOLINFO METAD ERMSD TORSION DISTANCE	colvar bias generic
19.016	Succinnic acid gamma polymorph	materials	Succinnic acid, conformers, polymorphs, metadynamics	Matteo Salvalaglio	ENDPLUMED PRINT UPPER_WALLS LOWER_WALLS COMBINE METAD MATHEVAL ENERGY CELL TORSION VOLUME	function colvar bias generic
25.026	Deciphering the Molecular Mechanisms of Startle Disease - the Role of the Asn46Lys Mutation in the Glycine Receptor	bio	metadynamics, glycine receptors, funnel metadynamics	Jacob Adam Clark	FUNNEL_PS METAD COM LOWER_WALLS UPPER_WALLS FUNNEL PRINT	bias funnel generic vatom
25.003	Surrogate Model CV	methods	Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding	Sompriya Chatterjee	DISTANCE OPES_METAD GROUP ENERGY TORSION ENDPLUMED COMMITTOR PYTORCH_MODEL MOLINFO COMBINE CUSTOM MATHEVAL WHOLEMOLECULES PRINT	generic core colvar function pytorch opes
24.029	Combination of OPES and OPES-Explore	methods	OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin	Dhiman Ray	OPES_METAD PYTORCH_MODEL MOLINFO COMBINE FIXEDATOM FLUSH UPPER_WALLS COORDINATION ENDPLUMED BIASVALUE MATHEVAL WHOLEMOLECULES POSITION RMSD LOWER_WALLS GROUP UNITS ENERGY FIT_TO_TEMPLATE CONTACTMAP DISTANCE OPES_METAD_EXPLORE METAD CENTER CUSTOM PRINT INCLUDE	generic core colvar setup bias function vatom pytorch opes
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	DISTANCE ENERGY METAD COORDINATIONNUMBER COMMITTOR TORSION BIASVALUE RESTRAINT MOLINFO MATHEVAL FLUSH RESTART PRINT	generic colvar setup bias function symfunc
24.006	Water vapor condensation	chemistry	metadynamics, homogeneous condensation, chemical potential	Shenghui Zhong	UNITS METAD COORDINATIONNUMBER DFSCLUSTERING CLUSTER_NATOMS CONTACT_MATRIX CLUSTER_PROPERTIES UPPER_WALLS PRINT	adjmat clusters generic setup bias symfunc
24.005	Learning Markovian Dynamics with Spectral Maps	methods	spectral map, collective variables, machine learning	Jakub Rydzewski	DISTANCE UNITS BIASVALUE CUSTOM PRINT	generic colvar setup bias function
23.045	Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state	bio	Path CVs Metadynamics, GPCRs activation transition	Vittorio Limongelli	DISTANCE METAD ALPHARMSD LOWER_WALLS PATHMSD MOLINFO UPPER_WALLS CONTACTMAP FUNCPATHMSD PRINT INCLUDE	generic colvar secondarystructure bias function
23.036	Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water?	bio	NaCl, nucleation, metadynamics	Ruiyu Wang	Q6 ENERGY METAD COORDINATIONNUMBER COMBINE MATHEVAL Q4 VOLUME PRINT	generic colvar bias function symfunc
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 METAD GHBFIX BIASVALUE ERMSD MOLINFO COMBINE WHOLEMOLECULES PRINT	bias colvar generic function
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	DISTANCE METAD READ MOLINFO DUMPGRID MATHEVAL REWEIGHT_METAD WHOLEMOLECULES CONVERT_TO_FES RMSD HISTOGRAM PRINT	generic colvar gridtools bias function
22.030	Mixing physics across temperatures with generative artificial intelligence	methods	REMD, Generative AI, DDPM	Yihang Wang	WHOLEMOLECULES TORSION PRINT	colvar generic
22.029	Angiotensin-1-7_Metadynamics	bio	Metadynamics, Angiotensin-(1-7), peptide	L.-América Chi	COORDINATION GROUP METAD LOWER_WALLS FLUSH WHOLEMOLECULES UPPER_WALLS GYRATION PRINT	bias colvar generic core
22.025	Bubble nucleation rate predictions in a Lennard-Jones fluid	materials	free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation	Kristof Bal	UNITS MOVINGRESTRAINT COORDINATIONNUMBER ANN COMMITTOR BIASVALUE UPPER_WALLS REWEIGHT_BIAS RESTRAINT CUSTOM LOAD FLUSH CONVERT_TO_FES DUMPGRID HISTOGRAM VOLUME PRINT	generic colvar annfunc setup gridtools bias function symfunc
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_PS DISTANCE METAD COM LOWER_WALLS WHOLEMOLECULES UPPER_WALLS FUNNEL PATHMSD PRINT	generic colvar bias funnel vatom
22.016	Homogeneous ice nucleation in an ab initio machine learning model of water	chemistry	ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces	Pablo Piaggi	OPES_METAD ENERGY AROUND CUSTOM UPPER_WALLS ENVIRONMENTSIMILARITY DUMPGRID HISTOGRAM VOLUME PRINT RESTART	generic envsim colvar setup gridtools volumes bias function opes
22.009	Glycosylation in calixarenes capsule	chemistry	Metadynamics, glycosylation, supramolecular catalysis	GiovanniMaria Piccini	COORDINATION DISTANCE UNITS GROUP BRIDGE DISTANCES ANGLE METAD LOWER_WALLS COMBINE MATHEVAL FIT_TO_TEMPLATE FLUSH WHOLEMOLECULES UPPER_WALLS RMSD PRINT	adjmat generic core multicolvar colvar setup bias function
22.003	Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling	methods	opes, metadynamics, reweighting, alanine, muller	Michele Invernizzi	PBMETAD OPES_METAD UNITS OPES_METAD_EXPLORE ENERGY METAD TORSION ENDPLUMED BIASVALUE LOWER_WALLS UPPER_WALLS CUSTOM POSITION ECV_UMBRELLAS_FILE OPES_EXPANDED ECV_MULTITHERMAL PRINT	generic colvar setup bias function opes
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 UNITS METAD TORSION COM LOWER_WALLS CUSTOM UPPER_WALLS PRINT	generic vatom colvar setup bias function
21.039	Deep learning the slow modes for rare events sampling	methods	collective variables, machine learning, slow modes, deep-tica, opes	Luigi Bonati	OPES_METAD PYTORCH_MODEL MOLINFO COMBINE FLUSH Q6 TORSION ENDPLUMED WHOLEMOLECULES OPES_EXPANDED RMSD ECV_MULTITHERMAL UNITS GROUP ENERGY LOAD ENVIRONMENTSIMILARITY CONTACTMAP DISTANCE VOLUME PRINT INCLUDE	generic core envsim colvar setup function pytorch opes symfunc
21.015	Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin	bio	metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module	Gaston Courtade	COORDINATION METAD RESTRAINT CENTER MATHEVAL WHOLEMOLECULES RESTART POSITION REWEIGHT_BIAS PRINT	generic vatom colvar setup bias function
21.013	Role of vibrational excitation in heterogeneous catalysis	chemistry	catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption	Kristof Bal	EXTERNAL UWALLS COORDINATIONNUMBER COMBINE REWEIGHT_METAD FLUSH UPPER_WALLS HISTOGRAM VES_LINEAR_EXPANSION COORDINATION CONVERT_TO_FES TD_GRID DUMPGRID LOWER_WALLS UNITS OPT_AVERAGED_SGD BF_CHEBYSHEV ANGLES LOAD DISTANCES DISTANCE METAD RESTRAINT REWEIGHT_BIAS PRINT	generic multicolvar ves colvar setup gridtools bias function symfunc
21.012	NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition	bio	funnel metadynamics	Jim Pfaendtner	FUNNEL_PS DISTANCE METAD COM LOWER_WALLS UPPER_WALLS FUNNEL PRINT	generic colvar bias funnel vatom
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
20.028	Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane	bio	metadynamics, KRas-4B, anionic membrane	Huixia Lu	DISTANCE METAD CENTER FIT_TO_TEMPLATE RESTART PRINT	generic colvar setup bias vatom
20.024	Gaussian Mixture Based Enhanced Sampling (GAMBES)	methods	enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias	Jayashrita Debnath	DISTANCES DISTANCE UNITS GROUP ENERGY TORSION LOWER_WALLS COMBINE LOAD UPPER_WALLS PRINT	generic core multicolvar colvar setup bias function
20.020	Parallel Bias Metadynamics	methods	pbmetad, trp-cage, folding	Max Bonomi	PBMETAD COORDINATION DIHCOR ALPHABETA MOLINFO WHOLEMOLECULES GYRATION PRINT INCLUDE	multicolvar bias colvar generic
20.017	FISST	methods	FISST, force, peptide, sampling, tempering	Glen Hocky	DISTANCE UNITS GROUP ENERGY FISST BIASVALUE RESTRAINT MATHEVAL GYRATION PRINT	generic core colvar setup bias fisst function
20.016	Predicting polymorphism in molecular crystals using orientational entropy	materials	metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy	Pablo Piaggi	GROUP METAD CENTER LOAD UPPER_WALLS VOLUME PRINT INCLUDE	generic core colvar setup bias vatom
20.011	Uremic toxin analysis	bio	metadynamics, uremic toxin, serum albumin	Jim Pfaendtner	COORDINATION DISTANCE GROUP DISTANCES CENTER WHOLEMOLECULES RESTART PRINT	generic core multicolvar colvar setup vatom
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	MOLINFO COMBINE REWEIGHT_METAD FLUSH UPPER_WALLS READ HISTOGRAM FUNCPATHMSD ENDPLUMED WHOLEMOLECULES CONVERT_TO_FES DUMPGRID LOWER_WALLS CONTACTMAP DISTANCE ABMD METAD COM PRINT	generic vatom colvar gridtools bias function
20.000	Muscarinic M2 receptor-ligand funnel metadynamics	bio	multiple walker metadynamics, well-tempered metadynamics, funnel metadynamics, MC-HLDA, GPCR, receptor, Adiabatic Bias MD	Riccardo Capelli	DISTANCE ABMD METAD CONVERT_TO_FES ENDPLUMED COM LOWER_WALLS READ COMBINE MATHEVAL REWEIGHT_METAD UPPER_WALLS DUMPGRID HISTOGRAM PRINT	generic colvar gridtools bias function vatom
19.071	Time-independent free energies from metadynamics via Mean Force Integration	methods	metadynamics, mean force integration, MFI, thermodynamic integration	Matteo Salvalaglio	EXTERNAL DISTANCE METAD TORSION COMMITTOR BIASVALUE REWEIGHT_BIAS DUMPGRID MATHEVAL REWEIGHT_METAD CONVERT_TO_FES READ HISTOGRAM PRINT	generic colvar gridtools bias function
19.056	maze	methods	maze, ligand unbinding	Jakub Rydzewski	MAZE_LOSS UNITS MAZE_OPTIMIZER_BIAS POSITION PRINT MAZE_SIMULATED_ANNEALING	maze setup generic colvar
19.051	Solid liquid interfacial free energy out of equilibrium	materials	metadynamics, nucleation, surface excess free energy	Gareth Tribello	UNITS FCCUBIC METAD AROUND ENDPLUMED CELL UPPER_WALLS PRINT LOWER_WALLS	generic colvar setup volumes bias symfunc
19.050	Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes	chemistry	metadynamics, membranes, Willard Chandler surface	Gareth Tribello	METAD REWEIGHT_BIAS UPPER_WALLS COMBINE DUMPGRID DISTANCE_FROM_CONTOUR CONVERT_TO_FES READ HISTOGRAM PRINT RESTART	generic setup gridtools bias function contour
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 ENDPLUMED MATHEVAL PRINT	bias colvar generic function
19.035	Dimerization of GPCRs from coarse-grained umbrella sampling	bio	Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization	Davide Provasi	DISTANCE GROUP TORSION COM RESTRAINT PRINT	generic core colvar bias vatom
19.029	WTE-metaD of FF domain of URNF1 C57D variant	bio	metadynamics, mutations, post-translational modification, ff domain	Elena Papaleo	GROUP METAD LOWER_WALLS ALPHABETA MOLINFO WHOLEMOLECULES UPPER_WALLS GYRATION PRINT	generic core multicolvar colvar bias
19.026	Ice Nucleation on Cholesterol Crystals	materials	forward flux sampling, crystal nucleation, water, ice, organic crystals	Gabriele Cesare Sosso	LOCAL_Q6 Q6 DFSCLUSTERING COMMITTOR ENDPLUMED MFILTER_MORE CLUSTER_NATOMS CONTACT_MATRIX FLUSH OUTPUT_CLUSTER CLUSTER_WITHSURFACE	adjmat clusters generic multicolvar symfunc
19.020	PTMetaD-WTE simulation of the Ntail IDP	bio	metadynamics, IDPs, protein folding	Mattia Bernetti	ENERGY METAD ALPHARMSD ENDPLUMED MOLINFO WHOLEMOLECULES GYRATION PRINT	generic bias colvar secondarystructure
19.014	MIL101(Cr) SBUs assembly	materials	MOFs, nucleation, self-assembly, metadynamics	Matteo Salvalaglio	DISTANCES METAD COORDINATIONNUMBER ENDPLUMED RESTART GYRATION PRINT	generic multicolvar colvar setup bias symfunc
19.005	Cmyc small molecule interaction	bio	metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP	Gabriella Heller	PBMETAD COORDINATION GROUP DISTANCE CS2BACKBONE METAINFERENCE ALPHABETA MOLINFO CENTER WHOLEMOLECULES GYRATION PRINT INCLUDE	generic core multicolvar colvar bias vatom isdb
19.003	EMMI ClpP	bio	metainference, cryo-EM	Max Bonomi	EMMI GROUP BIASVALUE MOLINFO PRINT	bias isdb generic core
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	DISTANCE LOWER_WALLS COM REWEIGHT_BIAS DUMPGRID CONVERT_TO_FES MOLINFO WHOLEMOLECULES HISTOGRAM FIXEDATOM PRINT UPPER_WALLS METAD	bias gridtools generic vatom colvar
25.027	Enhanced-sampling MD simulations of a protein-peptide complex integrating SAXS and XL-MS experimental information	bio	steered MD, metadynamics, SAXS, XL-MS, ensemble reconstruction	Mattia Bernetti	GYRATION DISTANCE INCLUDE SAXS CENTER MOLINFO WHOLEMOLECULES GROUP PRINT MOVINGRESTRAINT UPPER_WALLS METAD	bias generic isdb core vatom colvar
25.017	Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity	bio	EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase	Samuel Hoff	EMMIVOX MOLINFO WHOLEMOLECULES GROUP PRINT BIASVALUE	generic bias core isdb
25.016	Advancing in silico drug design with Bayesian refinement of AlphaFold models	bio	bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment	Samiran Sen	GROUP PRINT BAIES BIASVALUE	generic bias core isdb
25.013	Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices	bio	umbrella sampling, temperature ramping	Alexander Berlaga	GYRATION DISTANCE PYTORCH_MODEL RESTRAINT PRINT	generic bias colvar pytorch
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	DISTANCE CENTER ENDPLUMED OPES_METAD MOLINFO FIT_TO_TEMPLATE FIXEDATOM PRINT ANGLE CONTACTMAP WHOLEMOLECULES TORSION MATHEVAL CUSTOM UPPER_WALLS RMSD COORDINATION COMMITTOR GROUP COMBINE METAD	bias opes generic core vatom function 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	METAD COM MOLINFO ENERGY PRINT INCLUDE CONTACTMAP WHOLEMOLECULES TORSION PROJECTION_ON_AXIS OPES_METAD_EXPLORE LOWER_WALLS CONSTANT MATHEVAL ECV_MULTITHERMAL CUSTOM UPPER_WALLS RMSD WRAPAROUND COORDINATION GROUP OPES_EXPANDED RESTART BIASVALUE	bias opes generic setup core vatom function colvar
24.008	yCD Metadynamics	bio	volume-based MetaD, path CVs, infrequent MetaD, product release	James McCarty	DISTANCE COM ENDPLUMED CONVERT_TO_FES MOLINFO FIT_TO_TEMPLATE FIXEDATOM PRINT FLUSH INCLUDE CONTACTMAP PATH WHOLEMOLECULES DUMPGRID MATHEVAL REWEIGHT_METAD READ UPPER_WALLS RMSD WRAPAROUND COORDINATION COMMITTOR GROUP HISTOGRAM METAD	mapping bias gridtools generic core vatom function colvar
24.007	SWISH-X	bio	swish-x, SWISH-X, swish, expanded SWISH	Alberto Borsatto	INCLUDE CONTACTMAP MOLINFO ECV_MULTITHERMAL WHOLEMOLECULES ENERGY OPES_EXPANDED PRINT UPPER_WALLS	generic bias colvar opes
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	DISTANCE CENTER ENDPLUMED OPES_METAD MOLINFO FIT_TO_TEMPLATE ENERGY FIXEDATOM PRINT ANGLE INCLUDE CONTACTMAP WHOLEMOLECULES PYTORCH_MODEL LOWER_WALLS MATHEVAL CUSTOM UPPER_WALLS RMSD COORDINATION COMMITTOR GROUP COMBINE	bias opes generic core vatom function colvar pytorch
23.006	Transcription factor unbinding	bio	metadynamics, DNA, conformational changes	Malin Lüking	DISTANCE ANGLE CONTACTMAP ALPHARMSD COM DUMPFORCES MOLINFO PRINT METAD	bias secondarystructure generic vatom colvar
22.038	Enhanced Sampling Aided Design of Molecular Photoswitches	chemistry	reaction discovery, OPES explore, graph CV	Umberto Raucci	UNITS COORDINATION PYTORCH_MODEL CUSTOM PRINT OPES_METAD_EXPLORE	opes generic setup function colvar pytorch
22.036	Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction	bio	Well-tempered MetaDynamics with Hamiltonian Replica Exchange	Miroslav Krepl	LOAD GHBFIX MOLINFO COORDINATION FLUSH BIASVALUE GROUP COMBINE CUSTOM PRINT UPPER_WALLS METAD	bias generic setup core function colvar
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	GYRATION MOLINFO PBMETAD WHOLEMOLECULES TORSION	generic bias colvar
22.024	Conformational Entropy as a Potential Liability of Computationally Designed Antibodies	bio	metadynamics, conformational entropy, antibody, nanobody	Thomas Löhr	ALPHABETA COM ALPHARMSD ANTIBETARMSD MOLINFO PBMETAD WHOLEMOLECULES TORSION RESTART PRINT	bias secondarystructure generic setup vatom colvar multicolvar
22.022	Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir	bio	RMSD, protein-ligand interactions	Isabell Grothaus	PRINT RMSD	generic colvar
22.020	Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA	bio	RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics	Weiwei He	DISTANCE COM WHOLEMOLECULES GROUP TORSION PRINT METAD	bias generic core vatom colvar
22.012	Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT	bio	contact maps, protein-protein interactions	Isabell-Louise Grothaus	CENTER PRINT DISTANCE CONTACTMAP	generic colvar vatom
22.006	Peptide framework for screening the effects of amino acids on assembly	bio	metadynamics, peptides	Andrew White	GYRATION INCLUDE COM DUMPGRID REWEIGHT_BIAS CONVERT_TO_FES PRINT DISTANCES GROUP COMBINE HISTOGRAM METAD	bias gridtools generic core vatom function colvar multicolvar
22.005	Collective Variable for Metadynamics Derived from AlphaFold Output	bio	AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable	Vojtech Spiwok	LOAD WHOLEMOLECULES PRINT METAD	generic bias setup
21.050	N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity	methods	bio	Isabell Louise Grothaus	CENTER PRINT DISTANCE	generic colvar vatom
21.043	Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes	chemistry	well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability	Huixia Lu	METAD FIT_TO_TEMPLATE FIXEDATOM PRINT TORSION	generic bias colvar vatom
21.042	Peptoid-mediated Au nanocrystal growth	materials	parallel-bias metadynamics, peptoid, Au	Xin Qi	GYRATION DISTANCE COM MOLINFO PBMETAD PRINT UPPER_WALLS	generic bias colvar vatom
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	ENDPLUMED COORDINATION VOLUME COMBINE CUSTOM PRINT METAD	generic bias colvar function
21.023	Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling	methods	enhanced sampling, collective variables, machine learning	Jakub Rydzewski	DISTANCE INCLUDE CONSTANT UNITS REWEIGHT_METAD BIASVALUE ENERGY TORSION CUSTOM PRINT METAD	bias generic setup function colvar
21.019	Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations	materials	Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen	Matteo Salvalaglio	KDE DISTANCE COM MATHEVAL TORSIONS PRINT	gridtools generic vatom function colvar multicolvar
21.001	Substrate recognition and catalysis by glycosaminoglycan sulfotransferases	bio	metadynamics, well-tempered metadynamics, puckering, coordination	Tarsis Ferreira	RANDOM_EXCHANGES DISTANCE PUCKERING LOWER_WALLS INCLUDE DUMPGRID MOLINFO COORDINATION REWEIGHT_METAD WHOLEMOLECULES ENERGY GROUP HISTOGRAM PRINT UPPER_WALLS METAD	bias gridtools generic core colvar
20.030	Converging experimental and computational views of the knotting mechanism of the smallest knotted protein	bio	phi-values, transition state, knotted proteins	Cristina Paissoni	STATS MOLINFO COORDINATION WHOLEMOLECULES RESTRAINT COMBINE PRINT	function bias colvar generic
20.023	metadynminer and metadynminer3d	methods	metadynamics, visualization, R	Vojtech Spiwok	TORSION PRINT METAD	generic bias colvar
20.018	Free energy barriers from biased molecular dynamics simulations	methods	kinetics, free energy barriers, chemical reactions, nucleation, metadynamics	Kristof Bal	DENSITY DISTANCE CENTER CONVERT_TO_FES UNITS ENERGY PRINT FLUSH LOCAL_AVERAGE LOAD Q6 LOWER_WALLS DUMPGRID REWEIGHT_METAD VOLUME COORDINATIONNUMBER UPPER_WALLS SPRINT PAIRENTROPY REWEIGHT_BIAS CONTACT_MATRIX COORDINATION COMBINE HISTOGRAM METAD	bias symfunc adjmat gridtools generic setup sprint vatom volumes function colvar
20.007	Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics	bio	metadynamics, loop movement, artificial intelligence	Pratyush Tiwary	RMSD DISTANCE MOLINFO WHOLEMOLECULES COMBINE TORSION RESTART PRINT UPPER_WALLS METAD	bias generic setup function colvar
20.006	Class B GPCR activation mechanism	bio	metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	RMSD DISTANCE LOWER_WALLS CENTER MATHEVAL MOLINFO WHOLEMOLECULES ENERGY COMBINE PRINT UPPER_WALLS METAD	bias generic vatom function colvar
19.083	Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis	chemistry	metadynamics, chemical reactions, reaction discovery	Valerio Rizzi	ENDPLUMED UNITS UPPER_WALLS COMBINE DISTANCES GROUP COORDINATIONNUMBER RESTART PRINT FLUSH METAD	bias symfunc generic setup core function multicolvar
19.066	Finding ligand unbinding reaction pathways	methods	maze, ligand unbinding	Jakub Rydzewski	UNITS MAZE_OPTIMIZER_BIAS MAZE_LOSS POSITION MAZE_SIMULATED_ANNEALING PRINT	generic colvar setup maze
19.064	Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	GYRATION DISTANCE COM MOLINFO ENERGY PRINT UPPER_WALLS METAD	generic bias colvar vatom
19.062	Elucidating molecular design principles for charge-alternating peptides	bio	peptide folding, metadynamics, well-tempered ensemble, parallel tempering	Jim Pfaendtner	GYRATION WHOLEMOLECULES ENERGY PRINT METAD	generic bias colvar
19.061	Diffusion in porous materials	materials	metadynamics, porous materials, diffusion	Kim E. Jelfs	DISTANCE LOWER_WALLS COM CENTER GROUP RESTART PRINT UPPER_WALLS METAD	bias generic setup core vatom colvar
19.060	Neural networks-based variationally enhanced sampling	methods	ves, neural networks	Luigi Bonati	LOAD ENDPLUMED Q6 UNITS ENVIRONMENTSIMILARITY POSITION ENERGY TORSION PRINT	envsim symfunc generic setup colvar
19.054	MetaFEP	methods	metadynamics, chemistry, free energy perturbation	GiovanniMaria Piccini	DISTANCE LOWER_WALLS UNITS UPPER_WALLS ENERGY COMBINE PRINT FLUSH METAD	bias generic setup function colvar
19.046	Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding	bio	VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation	Faidon Brotzakis	FUNNEL RMSD LOWER_WALLS DISTANCE COM ALPHABETA MOLINFO BRIDGE REWEIGHT_METAD DISTANCES WHOLEMOLECULES GROUP COMBINE TORSION PRINT UPPER_WALLS METAD	bias adjmat generic core vatom function colvar multicolvar funnel
19.023	RECT	methods	metadynamics, replica exchange	Giovanni Bussi	GYRATION WHOLEMOLECULES TORSION PRINT METAD	generic bias colvar
26.004	Resolving the ambiguous binding site of quercetin at the calcineurin subunit junction using funnel metadynamics with deep learning collective variables	bio	metadynamics, funnel metadynamics, DeepTICA	Jason Loo	DISTANCE GROUP COM ENERGY FUNNEL_PS PYTORCH_MODEL UPPER_WALLS METAD WRAPAROUND WHOLEMOLECULES LOWER_WALLS RMSD FUNNEL MATHEVAL PRINT COORDINATION	funnel function core generic pytorch colvar vatom bias
26.000	OPES simulations of disordered proteins	bio	OPES, IDPs	Julian Streit	OPES_EXPANDED ENERGY ECV_MULTITHERMAL RESTART PRINT	generic opes colvar setup
25.009	Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water	chemistry	metadynamics, nitrate photolysis	Kam-Tung Chan	DISTANCE DUMPGRID GROUP READ RESTART REWEIGHT_METAD UPPER_WALLS METAD CUSTOM FLUSH HISTOGRAM PRINT COORDINATION	setup function core generic gridtools colvar bias
25.004	Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride	chemistry	OPES, OPES flooding, Catalysis, Ammonia Synthesis	Axel Tosello Gardini	DISTANCE UNITS GROUP COORDINATIONNUMBER COMMITTOR UPPER_WALLS DISTANCES ZDISTANCES CUSTOM FIXEDATOM FLUSH OPES_METAD PRINT	setup symfunc function opes core generic multicolvar colvar bias vatom
25.000	Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer	bio	metadynamics, pathCV	Sahithya Sridharan Iyer	DISTANCE GROUP COM MOLINFO RESTART METAD UPPER_WALLS FUNCPATHGENERAL WHOLEMOLECULES PRINT	setup function core generic colvar vatom bias
24.033	Transient interactions between the fuzzy coat and the cross-b core of brain-derived Ab42 filaments	bio	CryoEM, MEMMI, Metadynamics, Metainference, Ab42 Fibrils, structural ensemble	Maria Milanesi	DISTANCE GROUP COM EMMI MOLINFO ALPHARMSD UPPER_WALLS DUMPMASSCHARGE CENTER WHOLEMOLECULES RMSD PBMETAD DUMPATOMS COORDINATION BIASVALUE PRINT PARABETARMSD	core generic colvar secondarystructure isdb vatom bias
24.032	DeepLNE++	methods	PATHCV, OPES	Thorben Fröhlking	DISTANCE GROUP ENERGY TORSION LOAD COMBINE CUSTOM OPES_METAD PRINT COORDINATION	setup function opes core generic 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 GROUP MOLINFO ALPHARMSD TORSION COMBINE DIHCOR INCLUDE ANTIBETARMSD FLUSH WHOLEMOLECULES ENDPLUMED PARABETARMSD PBMETAD COORDINATION PRINT GYRATION	function core generic multicolvar secondarystructure colvar bias
24.000	Ammonia Decomposition on Non-stoichiometric Lithium Imide	chemistry	ammonia decomposition, non-stoichiometric lithium imide, machine learning interatomic potentials, enhanced sampling, heterogeneous catalysis	Francesco Mambretti	DISTANCE UNITS GROUP COORDINATIONNUMBER UPPER_WALLS ZDISTANCES FIXEDATOM FLUSH OPES_METAD PRINT	setup symfunc opes core generic multicolvar colvar bias vatom
23.046	Lasso Peptides - HLDA CV	bio	metadynamics, protein folding, HLDA, harmonic	Gabriel da Hora	DISTANCE UNITS METAD COMBINE WHOLEMOLECULES PRINT	setup function generic colvar bias
23.018	Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention	materials	metadynamics, surface binding, peptide adsorption	Kaylyn Torkelson	DISTANCE COM UPPER_WALLS PBMETAD PRINT GYRATION	colvar generic bias vatom
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 UNITS FIT_TO_TEMPLATE GROUP PYTORCH_MODEL TORSION UPPER_WALLS OPES_METAD_EXPLORE CUSTOM PATH FIXEDATOM CENTER WHOLEMOLECULES LOWER_WALLS OPES_METAD PRINT COORDINATION	setup function opes core generic mapping pytorch colvar bias vatom
23.008	PBMetaD simulations of Histatin5	bio	metadynamics, IDP, Rg, PPII	Francesco Pesce	GROUP MOLINFO TORSION WHOLEMOLECULES PBMETAD PRINT GYRATION	colvar core generic bias
23.007	Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains	bio	metadynamics, peptoids, parallel-bias metadynamics	Jim Pfaendtner	COM RESTRAINT TORSION INCLUDE WHOLEMOLECULES PBMETAD COORDINATION PRINT GYRATION	colvar generic bias vatom
22.043	Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES	bio	OPES, RNA, Tetraloop, Folding	Gül Zerze	OPES_EXPANDED ENERGY ECV_MULTITHERMAL ECV_UMBRELLAS_LINE WHOLEMOLECULES CONTACTMAP PRINT	opes colvar generic
22.040	From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure	bio	SARS-CoV-2, Spike, Omicron	Miłosz Wieczór	PCAVARS METAD UPPER_WALLS WHOLEMOLECULES LOWER_WALLS PRINT	generic mapping bias
22.034	Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods	materials	metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene	Matteo Salvalaglio	COMMITTOR CELL METAD UPPER_WALLS CUSTOM DRMSD LOWER_WALLS MATHEVAL PRINT	function colvar generic bias
21.051	Automatic learning of hydrogen-bond fixes in an AMBER RNA force field	methods	force field, RNA	Giovanni Bussi	ERMSD MOLINFO METAD COMBINE WHOLEMOLECULES BIASVALUE PRINT COORDINATION	function colvar generic bias
21.049	Multiple-path-metadynamics and PathMaps	methods	path-CV, metadynamics, multiple-walker, multiple paths, pathmap	Alberto Pérez-de-Alba-Ortíz	UNITS RESTRAINT TORSION UPPER_WALLS METAD COMBINE PRINT CUSTOM ENSEMBLE LOWER_WALLS CONSTANT LOAD MOVINGRESTRAINT	setup function generic colvar 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	TORSION METAD INCLUDE ENDPLUMED PBMETAD RANDOM_EXCHANGES PRINT	colvar generic bias
21.029	Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs	bio	metadynamics, small peptide, machine learning	Pratyush Tiwary	ENERGY EXTERNAL MOLINFO RESTART TORSION FLUSH PRINT	setup colvar generic bias
21.017	All-atom simulations of the Vav1 AD construct	bio	metadynamics, parallel-bias, well-tempered	Simone Orioli	GROUP MOLINFO ALPHARMSD RESTART REWEIGHT_BIAS METAD ALPHABETA WHOLEMOLECULES CONTACTMAP PBMETAD PRINT	setup core generic multicolvar secondarystructure colvar bias
20.031	Soft fluorescent nanoshuttles targeting receptors	chemistry	polymers, receptors, nanoparticles, fluorescent probes	Adriana Pietropaolo	CENTER WHOLEMOLECULES PBMETAD PRINT COORDINATION	colvar generic bias vatom
20.022	Unified Approach to Enhanced Sampling	methods	OPES, expanded ensembles, importance sampling	Michele Invernizzi	OPES_EXPANDED ENERGY VOLUME UPPER_WALLS POSITION ECV_MULTITHERMAL Q6 ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY UNITS CUSTOM WHOLEMOLECULES MATHEVAL LOAD MOLINFO TORSION ECV_LINEAR ENDPLUMED RMSD PRINT ECV_MULTITHERMAL_MULTIBARIC	setup symfunc function opes generic envsim colvar bias
19.075	PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python	other	Python, automatic differentiation	Toni Giorgino	DISTANCE GROUP RESTRAINT TORSION COMBINE ANGLE CUSTOM CENTER ENDPLUMED DUMPDERIVATIVES PRINT	function core generic colvar vatom bias
19.074	Asymmetric base pair opening in nucleic acids	bio	double helix, DNA, RNA, unwindability	Giovanni Bussi	DISTANCE RESTRAINT WHOLEMOLECULES ENDPLUMED LOWER_WALLS COORDINATION	colvar generic bias
19.043	Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	DISTANCE UNITS RESTART UPPER_WALLS DISTANCES COMBINE METAD FLUSH PRINT	setup function generic multicolvar colvar bias
19.032	Chemical reaction in solution using path collective variables based on coordination patterns	chemistry	chemical reactions, solutions, metadynamics, coordination patterns	Fabio Pietrucci	RESTART METAD UPPER_WALLS DISTANCES PATH FLUSH PRINT	setup generic mapping multicolvar bias
19.028	pRAVE	methods	RAVE, reaction coordinate, deep learning, metadynamics, kinetics	Pratyush Tiwary	DISTANCE COM EXTERNAL COMMITTOR RESTART TORSION COMBINE ALPHABETA WHOLEMOLECULES PRINT	setup function generic multicolvar colvar bias vatom
26.002	A Transferable and Robust Computational Framework for Class A GPCR Activation Free Energies	bio	OneOPES, GPCR, ADRB1, activation, euclidean path, microswitches, conformational changes, allostery	Valerio Rizzi	PRINT OPES_METAD_EXPLORE ECV_MULTITHERMAL CENTER CUSTOM OPES_EXPANDED COORDINATION PATHMSD UPPER_WALLS GROUP RMSD DISTANCE LOWER_WALLS VOLUME PATH ENERGY	function mapping bias opes colvar core vatom generic
25.030	Committor Regularization	methods	metadynamics, enhanced sampling, mlcvs, committor, machine learning	Florian Dietrich	PRINT METAD MOVINGRESTRAINT UNITS	setup bias 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	PRINT OPES_METAD_EXPLORE FIT_TO_TEMPLATE MATHEVAL CENTER COORDINATION UPPER_WALLS GROUP FIXEDATOM DISTANCE ANGLE ENERGY WHOLEMOLECULES	function bias opes colvar core vatom 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	PRINT DISTANCES OPES_METAD_EXPLORE ECV_MULTITHERMAL CENTER CUSTOM OPES_EXPANDED COORDINATION PATHMSD GHOST UPPER_WALLS GROUP RMSD DISTANCE LOWER_WALLS ENERGY	function multicolvar bias opes colvar core vatom 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	PRINT WHOLEMOLECULES COORDINATION HISTOGRAM TORSION GROUP CONVERT_TO_FES DISTANCE ANGLE DUMPGRID	gridtools colvar core generic
24.019	Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning	bio	OPES, machine learning, protein folding, adaptive sampling	Mingyuan Zhang	PRINT COMBINE CUSTOM OPES_METAD ALPHARMSD COORDINATION GYRATION MOLINFO TORSION DISTANCE WHOLEMOLECULES	secondarystructure function opes colvar generic
24.018	A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations	chemistry	prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning	Léon HUET	PRINT DISTANCE	colvar generic
24.009	Weighted Shape Gaussian Mixture Models	bio	metadynamics, clustering	Glen Hocky	PRINT UNITS GROUP METAD TORSION	setup bias colvar core 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	PRINT FIT_TO_TEMPLATE COMBINE ALPHARMSD MOLINFO METAD POSITION ANN WHOLEMOLECULES	annfunc secondarystructure function bias colvar generic
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	PRINT WRAPAROUND STATS CENTER MOLINFO UPPER_WALLS GROUP ENSEMBLE RMSD DISTANCE BIASVALUE SAXS	function bias colvar core vatom isdb generic
23.025	Probing ion binding to G-quadruplexes and related events	chemistry	metadynamics, repulsive potential, nucleic acids, G-quadruplexes	Marcelo Poleto	PRINT DISTANCES FIT_TO_TEMPLATE UNITS WRAPAROUND DISTANCE MATHEVAL FLUSH UPPER_WALLS GROUP METAD DUMPATOMS LOWER_WALLS POSITION COM RESTART WHOLEMOLECULES	setup function multicolvar bias colvar core vatom generic
23.005	A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs	bio	metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A	Timothy Clark	PRINT MATHEVAL DUMPGRID REWEIGHT_METAD READ MOLINFO HISTOGRAM METAD RMSD DISTANCE CONVERT_TO_FES WHOLEMOLECULES	function bias colvar gridtools generic
23.002	Critical comparison of general-purpose collective variables for crystal nucleation	methods	metadynamics, umbrella sampling, commitor, entropy, PIV	Julien Lam	PRINT Q6 UNITS LOCAL_AVERAGE CUSTOM PAIRENTROPY FUNCPATHMSD UPPER_WALLS PIV METAD Q4 RESTRAINT VOLUME ENERGY	setup function bias piv colvar symfunc gridtools generic
22.044	Colloid Crystallisation Analyses	materials	Q4, Q6, Pair Entropy, DFS	Aaron Finney	PRINT Q6 LOCAL_AVERAGE COMBINE LOCAL_Q6 MFILTER_LESS CONTACT_MATRIX MFILTER_MORE DFSCLUSTERING GROUP CLUSTER_NATOMS Q4 COORDINATIONNUMBER LOCAL_Q4	function clusters multicolvar adjmat symfunc core generic
22.031	Rare Event Kinetics from Adaptive Bias Enhanced Sampling	methods	OPES Flooding, Kinetics, Rate, OPES, Machine Learning	Dhiman Ray	PRINT RMSD ENERGY CUSTOM INCLUDE DISTANCE POSITION BIASVALUE UNITS COMBINE CONSTANT MOLINFO PYTORCH_MODEL GROUP COMMITTOR ENDPLUMED OPES_METAD TORSION CONTACTMAP WHOLEMOLECULES	setup function bias colvar core opes generic pytorch
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	PRINT ALPHABETA COORDINATION ALPHARMSD FLUSH MOLINFO UPPER_WALLS TORSION METAD DISTANCE ANGLE WHOLEMOLECULES	secondarystructure multicolvar bias colvar generic
21.047	Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations	materials	pair entropy, metadynamics, ves, solids, crystallization	Pablo Piaggi	PRINT BF_LEGENDRE COMBINE TD_WELLTEMPERED PAIRENTROPY METAD OPT_AVERAGED_SGD VES_LINEAR_EXPANSION VOLUME LOAD RESTART ENERGY	setup function bias ves colvar gridtools generic
21.045	QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP)	chemistry	metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange	Denis Maag	PRINT COMBINE DISTANCE COORDINATION UPPER_WALLS METAD COORDINATIONNUMBER LOWER_WALLS	function bias colvar symfunc 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	PRINT DIHCOR PARABETARMSD COORDINATION ALPHARMSD GYRATION MOLINFO UPPER_WALLS ANTIBETARMSD GROUP METAD LOWER_WALLS RANDOM_EXCHANGES ENERGY WHOLEMOLECULES	secondarystructure multicolvar bias colvar core generic
21.031	Photo-switchable sulfonulureas in KATP channel	bio	metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels	Katarzyna Walczewska-Szewc	PRINT UNITS UPPER_WALLS METAD DISTANCE LOWER_WALLS COM WHOLEMOLECULES	setup bias colvar vatom generic
21.009	Nucleation rates from small scale atomistic simulations and transition state theory	materials	kinetics, free energy barriers, nucleation, droplets, metadynamics	Kristof Bal	PRINT MOVINGRESTRAINT UNITS REWEIGHT_METAD FLUSH UPPER_WALLS HISTOGRAM METAD CONVERT_TO_FES COORDINATIONNUMBER LOAD COMMITTOR DUMPGRID	setup bias symfunc gridtools generic
21.006	OPES, On-the-fly Probability Enhanced Sampling Method	methods	opes, alanine dipeptide, well-tempered, multithermal, multiumbrella	Michele Invernizzi	PRINT ECV_MULTITHERMAL ECV_UMBRELLAS_LINE OPES_EXPANDED ENDPLUMED OPES_METAD TORSION ENERGY	opes colvar generic
20.029	High Conformational Flexibility of the E2F1/DP1/DNA complex	bio	SAXS, protein-DNA complex, hySAXS, ensemble determination	Cristina Paissoni	PRINT SAXS STATS CENTER INCLUDE MOLINFO GROUP ENSEMBLE DISTANCE RESTRAINT BIASVALUE WHOLEMOLECULES	function bias colvar core vatom isdb generic
20.015	Rational design of ASCT2 inhibitors using an integrated experimental-computational approach	bio	ASCT2 transporter, small-molecules, cryo-EM, metainference	Max Bonomi	PRINT EMMIVOX MOLINFO GROUP DUMPATOMS LOAD BIASVALUE WHOLEMOLECULES	setup bias core isdb generic
20.009	The dynamics of linear polyubiquitin	bio	saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics	Carlo Camilloni	PRINT ALPHABETA DISTANCE STATS CENTER METAINFERENCE FLUSH GYRATION MOLINFO TORSION ENSEMBLE PBMETAD SAXS WHOLEMOLECULES	function multicolvar bias colvar vatom isdb generic
20.001	Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins	bio	metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals	Carlo Camilloni	PRINT ALPHABETA CS2BACKBONE ENDPLUMED FLUSH MOLINFO UPPER_WALLS ANTIBETARMSD GROUP PBMETAD LOWER_WALLS BIASVALUE WHOLEMOLECULES	secondarystructure multicolvar bias core isdb generic
19.058	Constrained MD for maintaining a cavity in a calculation	chemistry	constrained MD, porous molecules, porosity, cavity	Kim Jelfs	PRINT MOVINGRESTRAINT DISTANCES INPLANEDISTANCES FLUSH COM RESTART	setup multicolvar bias vatom generic
19.048	Understanding Ligand Binding Selectivity in a Prototypical GPCR Family	bio	metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	PRINT MATHEVAL CONSTANT UPPER_WALLS METAD DISTANCE LOWER_WALLS COM BIASVALUE WHOLEMOLECULES	function bias colvar vatom generic
19.038	native state dynamics of human and mouse b2m	bio	metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation	Carlo Camilloni	PRINT ALPHABETA CS2BACKBONE ENDPLUMED FLUSH MOLINFO UPPER_WALLS ANTIBETARMSD GROUP PBMETAD LOWER_WALLS RESTART BIASVALUE WHOLEMOLECULES	secondarystructure setup multicolvar bias core isdb generic
19.036	Thermodynamics and kinetics of G protein-coupled receptor activation	bio	metadynamics, allostery, receptor conformation, GPCR, pharmacology	Davide Provasi	PRINT ENDPLUMED FUNCPATHMSD METAD RMSD DISTANCE CONTACTMAP COM WHOLEMOLECULES	function bias colvar vatom generic
19.019	FA-MetaD-JCP-Wang-et-al	bio	Frequency adaptive metadynamics; peptide	Kresten Lindorff-Larsen	PRINT ALPHABETA COMBINE FLUSH MOLINFO METAD COMMITTOR	bias multicolvar function generic
19.017	Ligand binding pathways exploration	bio	metadynamics, ligand binding	Riccardo Capelli	PRINT FIT_TO_TEMPLATE WRAPAROUND MATHEVAL DUMPGRID ENDPLUMED REWEIGHT_METAD COORDINATION FLUSH READ UPPER_WALLS HISTOGRAM GROUP METAD CONVERT_TO_FES POSITION COM WHOLEMOLECULES	vatom function bias colvar core gridtools generic
19.015	Ibuprofen conformational dynamics and thermodynamics surface	materials	Ibuprofen, crystal, surface, solvents, conformers, metadynamics	Matteo Salvalaglio	PRINT CENTER UPPER_WALLS TORSION METAD DISTANCE LOWER_WALLS COMMITTOR	vatom colvar bias generic
19.000	VesDeltaF	methods	VES, convergence, suboptimal CVs	Michele Invernizzi	PRINT UNITS ENDPLUMED VES_DELTA_F TORSION METAD POSITION LOAD RESTART ENERGY	setup bias ves colvar generic
26.001	Molecular simulations Alx riboswitch	bio	RNA, riboswitch	Giovanni Bussi	MOLINFO DISTANCE RESTRAINT PRINT MOVINGRESTRAINT ERMSD MATHEVAL	generic function bias colvar
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	CENTER WHOLEMOLECULES LOWER_WALLS DISTANCE UPPER_WALLS GROUP GYRATION COMBINE PRINT COORDINATION MATHEVAL METAD	function core bias colvar vatom generic
25.018	Metainference simulation for dimerization of RNA binding protein	bio	Metainference, Metadynamics, SAXS, protein dimer	Debadutta Patra	MOLINFO CENTER WHOLEMOLECULES FLUSH DISTANCE UPPER_WALLS PRINT TORSION SAXS STATS PBMETAD METAINFERENCE ENSEMBLE GYRATION	function bias isdb colvar vatom generic
25.014	Atomic resolution ensembles of intrinsically disordered proteins with Alphafold	bio	bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement	Vincent Schnapka	BAIES GROUP PRINT BIASVALUE	generic core isdb bias
25.010	Kinetic rates calculation with Ratchet&Pawl MD	methods	kinetics, ligand binding, ABMD, ratchet&pawl MD	Riccardo Capelli	WHOLEMOLECULES FLUSH COMMITTOR DISTANCE GROUP PRINT ABMD COM	core bias colvar vatom generic
24.026	Constant pH metadynamics of RNA oligomers	bio	metadynamics, pH, RNA	Giovanni Bussi	MOLINFO PUCKERING RESTART PRINT TORSION METAD	generic bias colvar setup
24.003	Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations	chemistry	steered molecular dynamics, foldamers, peptoids, bio-inspired	Kaylyn Torkelson	WHOLEMOLECULES INCLUDE DISTANCE PRINT ALPHABETA TORSION MOVINGRESTRAINT COORDINATION GYRATION COM	bias multicolvar colvar vatom generic
23.030	Data Driven Classification of Ligand Unbinding Pathways	bio	OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time	Dhiman Ray	COMMITTOR FLUSH LOWER_WALLS ENERGY CUSTOM DISTANCE ENDPLUMED WRAPAROUND UNITS COORDINATION MATHEVAL FIT_TO_TEMPLATE UPPER_WALLS GROUP TORSION COM MOLINFO CENTER WHOLEMOLECULES OPES_METAD PRINT POSITION OPES_METAD_EXPLORE BIASVALUE	function opes setup core bias colvar vatom generic
23.022	A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar	methods	collective variables, machine learning, toy model	Enrico Trizio	PYTORCH_MODEL CUSTOM ENDPLUMED UPPER_WALLS OPES_METAD UNITS PRINT POSITION BIASVALUE LOWER_WALLS	function opes setup bias colvar generic pytorch
23.020	FEP simulations of ATOX1 homodimer	chemistry	parallel bias metadynamics, FEP, free-energy of metal ion dissociation	Adriana Pietropaolo	CONSTANT WHOLEMOLECULES DISTANCE ANGLE PRINT PBMETAD BIASVALUE MATHEVAL	generic function bias colvar
22.042	Metadynamics of NSP10 and variants	bio	metadynamics, NSP10, crystal structure, variants	Shozeb Haider	METAD PRINT TORSION	generic bias colvar
22.039	Driving and characterizing nucleation of urea and glycine polymorphs in water	bio	metadynamics, nucleation, amino acids, polymorphism	Eric Beyerle	CENTER INCLUDE Q6 GROUP LOAD PAIRENTROPY COMBINE PRINT COORDINATIONNUMBER MATHEVAL METAD Q4	function gridtools setup core bias symfunc vatom generic
22.017	Water regulates the residence time of Benzamidine in Trypsin	bio	ligand binding, water, opes, benzamidine trypsin, unbinding rates, machine learning, Deep-LDA, Deep-TICA	Narjes Ansari	PYTORCH_MODEL CENTER CUSTOM WHOLEMOLECULES COMMITTOR DISTANCE FIT_TO_TEMPLATE UPPER_WALLS GROUP OPES_METAD PRINT FIXEDATOM COORDINATION RMSD LOWER_WALLS MATHEVAL	function opes core bias colvar vatom generic pytorch
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	WHOLEMOLECULES ENDPLUMED UPPER_WALLS GROUP GYRATION PRINT ALPHABETA LOWER_WALLS METAD	core bias multicolvar colvar generic
21.044	NaCl nucleation	chemistry	metadynamics, DFS clustering	Aaron Finney	INSPHERE HISTOGRAM DUMPGRID Q6 GROUP MFILTER_MORE COMBINE PRINT DFSCLUSTERING COORDINATIONNUMBER FIXEDATOM CLUSTER_NATOMS CONTACT_MATRIX LOCAL_Q6 METAD CLUSTER_DISTRIBUTION	clusters generic function gridtools core bias adjmat volumes multicolvar vatom symfunc
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	MOLINFO WHOLEMOLECULES DISTANCE RESTART GROUP UPPER_WALLS PRINT EMMI BIASVALUE COM	setup core bias isdb colvar vatom generic
21.026	Probing allosteric regulations with coevolution-driven molecular simulations	bio	metadynamics, coevolution, allostery, adenylate cyclase	Francesco Colizzi	WHOLEMOLECULES DISTANCE UPPER_WALLS UNITS PRINT PATHMSD METAD COM	setup bias colvar vatom generic
21.018	Localized Volume-based Metadynamics	bio	LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification	Riccardo Capelli	FLUSH REWEIGHT_METAD CONVERT_TO_FES RMSD DISTANCE ENDPLUMED COORDINATION MATHEVAL HISTOGRAM DUMPGRID UPPER_WALLS GROUP FIXEDATOM COM WHOLEMOLECULES PRINT POSITION READ METAD	function gridtools core bias colvar vatom generic
21.016	MD SAXS GTPase associated center	bio	metadynamics, RNA, folding, SAXS	Giovanni Bussi	MOLINFO CUSTOM WHOLEMOLECULES INCLUDE UPPER_WALLS GROUP GYRATION PRINT SAXS ERMSD LOWER_WALLS METAD	function core bias isdb colvar 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	MOLINFO CENTER DISTANCE RESTART PRINT TORSION ABMD ERMSD	setup bias colvar vatom 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	CONSTANT MOLINFO WHOLEMOLECULES INCLUDE DISTANCE FUNCPATHGENERAL UPPER_WALLS GROUP CONTACTMAP LOAD PRINT BIASVALUE LOWER_WALLS METAD COM MATHEVAL PROJECTION_ON_AXIS	function setup core bias colvar vatom generic
20.004	Data-driven collective variables for enhanced sampling	methods	collective variables, machine learning, deep-lda	Luigi Bonati	PYTORCH_MODEL FLUSH DISTANCE ENDPLUMED UPPER_WALLS GROUP OPES_METAD UNITS PRINT LOAD TORSION LOWER_WALLS COM MATHEVAL	opes function setup core bias colvar vatom generic pytorch
19.082	Ammonia Borane Dehydrogenation	chemistry	metadynamics, reaction discovery, hydrogen production, chemistry	Valerio Rizzi	EXTERNAL FLUSH ENDPLUMED RESTART GROUP UNITS PRINT COMBINE COORDINATIONNUMBER METAD	function setup core bias symfunc generic
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	OPT_DUMMY RESTART Q6 CONVERT_TO_FES LOWER_WALLS ENERGY TD_MULTITHERMAL_MULTIBARIC TD_WELLTEMPERED VOLUME COMBINE REWEIGHT_BIAS MATHEVAL REWEIGHT_TEMP_PRESS HISTOGRAM VES_LINEAR_EXPANSION DUMPGRID UPPER_WALLS LOAD CELL PRINT OPT_AVERAGED_SGD BF_LEGENDRE READ	generic function gridtools setup bias colvar ves symfunc
19.080	Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium	methods	ves, variationally enhanced sampling, vibrational excitation, chemical reactions	Kristof Bal	TD_WELLTEMPERED EXTERNAL HISTOGRAM FLUSH DISTANCE VES_LINEAR_EXPANSION DUMPGRID UPPER_WALLS ANGLE UNITS PRINT COMBINE OPT_AVERAGED_SGD COORDINATION CONVERT_TO_FES LOWER_WALLS TD_GRID BF_CHEBYSHEV	function gridtools setup bias colvar ves 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	ENDPLUMED UNITS PRINT MOVINGRESTRAINT GYRATION	generic bias colvar setup
19.067	Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways	bio	metadynamics, ligand unbinding	Jakub Rydzewski	UPPER_WALLS RESTART UNITS PRINT PATHMSD LOWER_WALLS METAD	generic bias colvar setup
19.039	Funnel Metadynamics	bio	funnel-metadynamics, absolute binding free energy, ligand-receptor complexes	Vittorio Limongelli	FUNNEL_PS WHOLEMOLECULES DISTANCE UPPER_WALLS FUNNEL PRINT RMSD LOWER_WALLS METAD COM	bias funnel colvar vatom generic
19.025	Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide	bio	metainference, NMR, protein dynamics, force-fields	Carlo Camilloni	MOLINFO CS2BACKBONE WHOLEMOLECULES FLUSH RDC ENDPLUMED PRINT TORSION STATS JCOUPLING PBMETAD BIASVALUE METAINFERENCE ENSEMBLE GYRATION	function bias isdb colvar generic
19.022	eABF simulation of NANMA (alanine dipeptide)	methods	eABF, DRR, alanine dipeptide	Haochuan Chen	TORSION PRINT DRR	generic drr colvar
19.009	RNA tetraloops folding	bio	metadynamics, RNA, folding	Giovanni Bussi	MOLINFO WHOLEMOLECULES ENDPLUMED PRINT ERMSD RMSD METAD	generic bias colvar
25.011	Chiral perovskite nucleation	chemistry	metadynamics, chiral perovskites, nucleation	Adriana Pietropaolo	PRINT UNITS MULTI_RMSD RESTART MATHEVAL PBMETAD UPPER_WALLS LOWER_WALLS DISTANCE	bias colvar generic function setup
25.005	Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations	chemistry	WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD	Vikas Tiwari, Tarak Karmakar	DISTANCES PRINT UNITS COORDINATIONNUMBER COORDINATION FLUSH FIXEDATOM COM COMBINE UPPER_WALLS GROUP LOWER_WALLS ANGLE RESTRAINT DISTANCE METAD	bias colvar core multicolvar symfunc generic function setup vatom
23.039	Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation	chemistry	metadynamics, ligand dissociation	Eric Beyerle	DUMPMASSCHARGE MOLINFO PRINT FIXEDATOM COMBINE UPPER_WALLS CENTER RESTRAINT DISTANCE METAD	bias colvar generic function vatom
23.037	Estimating binding free energy of solid binding peptides without extensive sampling	bio	metadynamics, solid binding peptides	Xin Qi	PRINT MOLINFO GYRATION COM PBMETAD UPPER_WALLS LOWER_WALLS DISTANCE	generic bias colvar vatom
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	PRINT READ EXTRACV TORSION METAD	generic colvar bias
22.015	Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome	bio	photodynamics, bacteriophytochrome, variationally enhanced sampling	Jakub Rydzewski	TD_UNIFORM VES_LINEAR_EXPANSION PRINT OPT_AVERAGED_SGD BF_FOURIER TORSION	ves generic colvar
21.052	On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets	materials	Ibuprofen, unbinding, WTmetaD	Matteo Salvalaglio	PRINT COORDINATIONNUMBER TORSION COMMITTOR ENDPLUMED CENTER DISTANCE METAD	bias colvar symfunc generic vatom
21.014	how to determine statistically accurate conformational ensembles	bio	metadynamics, metainference, errors, cv, SAXS, ensemble determination	Cristina Paissoni	ENSEMBLE PRINT MOLINFO ANTIBETARMSD ALPHABETA TORSION CONTACTMAP GYRATION SAXS PBMETAD BIASVALUE STATS CENTER WHOLEMOLECULES METAD	bias colvar isdb multicolvar secondarystructure generic function vatom
19.069	Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen	materials	ibuprofen, crystal, solvent, surface	Matteo Salvalaglio	PRINT INCLUDE ENDPLUMED GROUP CENTER DISTANCE	generic vatom colvar core
19.068	Rethinking Metadynamics	methods	metadynamics, opes, convergence	Michele Invernizzi	PRINT POSITION UNITS EXTERNAL OPES_METAD TORSION ENDPLUMED METAD	opes bias colvar generic setup
19.057	SAXS ensembles using Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics	Cristina Paissoni	ENSEMBLE PRINT MOLINFO ALPHABETA INCLUDE SAXS COORDINATION MATHEVAL PBMETAD ENDPLUMED COMBINE BIASVALUE GROUP CENTER ANGLE STATS WHOLEMOLECULES	bias colvar isdb multicolvar generic vatom function core
19.010	Multi-domain protein dynamics	bio	metainference, NMR, protein dynamics	Carlo Camilloni	ENSEMBLE PRINT MOLINFO DIHCOR CENTER ALPHABETA TORSION DHENERGY PBMETAD ENDPLUMED UPPER_WALLS GROUP METAINFERENCE STATS RESTRAINT WHOLEMOLECULES RDC DISTANCE	bias colvar isdb core multicolvar generic function vatom
25.022	Imidazole Diffusion in SALEM-2 MOF	materials	OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials	Sudheesh Kumar Ethirajan	DISTANCES MOLINFO PROJECTION_ON_AXIS DISTANCE UNITS GROUP ENDPLUMED OPES_METAD PRINT CENTER WHOLEMOLECULES	setup core vatom generic opes multicolvar colvar
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	VOLUME MOLINFO TORSION PBMETAD INCLUDE ENERGY DISTANCE GYRATION DUMPATOMS UPDATE_IF RESTART READ PRINT CENTER WHOLEMOLECULES	bias vatom generic colvar setup
24.028	All-atom simulations of RNA-membrane interactions	bio	metadynamics, membrane, RNA	Giovanni Bussi	DISTANCES COMBINE MOLINFO UPPER_WALLS DISTANCE GYRATION METAD POSITION SORT LOWER_WALLS GROUP GHOST PUCKERING MATHEVAL PRINT CENTER WHOLEMOLECULES	bias core vatom generic multicolvar function colvar
24.004	Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables	materials	metadynamics, nucleation, machine learning	Ziyue Zou	LOAD METAD GROUP RESTART INCLUDE PRINT	core generic bias setup
24.002	Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes	chemistry	metadynamics, ligand design, solvent extraction	Xiaoyu Wang	PRINT METAD UNITS RESTART TORSION	colvar setup bias 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	COMMITTOR COMBINE TORSION CUSTOM FLUSH UPPER_WALLS DISTANCE UNITS LOWER_WALLS OPES_METAD PRINT	setup bias generic opes function colvar
23.041	Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference	methods	EMMIVox, cryo-EM, single-structure refinement, ensemble refinement, Bayesian inference, B-factors, structural ensembles	Samuel Hoff	EMMIVOX MOLINFO INCLUDE UPPER_WALLS DISTANCE WRAPAROUND GROUP BIASVALUE PRINT WHOLEMOLECULES	bias core generic isdb colvar
23.040	Supramolecular capsules assembly dynamics	chemistry	Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics	Riccardo Capelli	DISTANCES CUSTOM FLUSH DISTANCE POSITION COM METAD UNITS GROUP PRINT CENTER WHOLEMOLECULES	bias setup core vatom generic multicolvar function colvar
23.038	Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor	bio	protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics	Timothy Clark	MOLINFO DISTANCE METAD RMSD MATHEVAL PRINT WHOLEMOLECULES	colvar function bias generic
23.024	Permutationally Invariant Networks for Enhanced Sampling (PINES)	methods	collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent	Nicholas Herringer	LOAD PBMETAD PRINT	generic bias setup
23.021	Into the Dynamics of Rotaxanes at Atomistic Resolution	materials	metadynamics, rotaxanes, molecular shuttles, molecular machines	Luigi Leanza	TORSION CUSTOM UPPER_WALLS DISTANCE FIXEDATOM METAD MATHEVAL PRINT CENTER	bias vatom generic function colvar
23.014	Structural basis of dimerization of chemokine receptors CCR5 and CXCR4	bio	metadynamics, oligomerization, chemokine receptors, GPCR, membrane	Vittorio Limongelli	COMBINE TORSION FLUSH UPPER_WALLS DISTANCE COM METAD PRINT WHOLEMOLECULES	bias vatom generic function colvar
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 PRINT METAD	generic multicolvar 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	CUSTOM FLUSH DISTANCE COM METAD UNITS BIASVALUE DRR PRINT	bias setup drr vatom generic function colvar
22.021	Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn Løland Bore	UPPER_WALLS OPES_EXPANDED LOWER_WALLS INCLUDE ECV_UMBRELLAS_LINE PRINT ENVIRONMENTSIMILARITY	opes envsim bias generic
22.004	Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques	chemistry	reaction discovery, OPES, collective variables	Umberto Raucci	LOAD COORDINATION CUSTOM UPPER_WALLS DISTANCE COM UNITS PYTORCH_MODEL OPES_METAD_EXPLORE GROUP LOWER_WALLS MATHEVAL OPES_METAD PRINT	bias setup core vatom generic opes pytorch function colvar
21.037	Molecular Dynamics simulations of RBD/hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain	Max Bonomi	RMSD DISTANCE PRINT	generic colvar
21.033	Multiple-path-metadynamics applied to DNA base-pairing transitions	bio	path-CV, metadynamics, multiple-walker, dna	Alberto Pérez-de-Alba-Ortíz	COMBINE UPPER_WALLS CONSTANT METAD RESTRAINT INCLUDE MOVINGRESTRAINT PRINT	bias function generic
21.028	From Enhanced Sampling to Reaction Profiles	methods	collective variables, multi-state, machine learning, Deep-TDA	Enrico Trizio	FIXEDATOM ENDPLUMED MATHEVAL DISTANCES LOAD ANGLE LOWER_WALLS PYTORCH_MODEL UNITS OPES_METAD TORSION CENTER UPPER_WALLS FIT_TO_TEMPLATE GROUP PRINT WHOLEMOLECULES COORDINATION DISTANCE	bias core vatom generic opes pytorch colvar multicolvar function setup
21.020	Reweighted Jarzynski sampling	methods	free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions	Kristof Bal	ANN COORDINATIONNUMBER OPT_AVERAGED_SGD RESTRAINT REWEIGHT_METAD BF_CHEBYSHEV HISTOGRAM LOAD CONSTANT UNITS VES_LINEAR_EXPANSION OPES_METAD COMBINE CONVERT_TO_FES CUSTOM UPPER_WALLS METAD BIASVALUE PRINT TD_WELLTEMPERED FLUSH DISTANCE REWEIGHT_BIAS DUMPGRID MOVINGRESTRAINT	symfunc bias ves generic opes colvar annfunc function gridtools setup
21.011	CmuMD simulations of NaCl(aq) at graphite	chemistry	CmuMD, DFS clustering	Aaron Finney	LOAD COORDINATIONNUMBER FIXEDATOM RESTRAINT DENSITY CONTACT_MATRIX GROUP DFSCLUSTERING CLUSTER_DISTRIBUTION DUMPGRID MFILTER_MORE MULTICOLVARDENS CLUSTER_NATOMS PRINT AROUND	symfunc bias core vatom volumes clusters generic adjmat multicolvar gridtools setup
21.005	Crystallization Collective Variable	methods	Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA	Tarak Karmakar	LOAD FLUSH UPPER_WALLS LOWER_WALLS PYTORCH_MODEL GROUP MATHEVAL OPES_METAD PRINT	bias core generic opes pytorch function setup
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 COM GROUP PRINT WHOLEMOLECULES	core vatom generic colvar
20.032	Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil	materials	clustering, conformational isomers	Matteo Salvalaglio	ENDPLUMED TORSION PRINT	colvar generic
20.027	Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery	bio	SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery	Khaled Abdel-Maksoud	DISTANCE TORSION PRINT METAD	generic bias colvar
19.065	Molecular Enhanced Sampling with Autoencoders	methods	enhanced sampling, collective variables, deep learning	Wei Chen	COMBINE ANN COM POSITION RESTRAINT	bias vatom annfunc function colvar
19.030	Coarse-Grained MetaDynamics (CG-MetaD)	bio	Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy	Vittorio Limongelli	UPPER_WALLS DISTANCE COM METAD LOWER_WALLS PRINT WHOLEMOLECULES	generic vatom bias colvar
25.024	Sampling glycan-glycan interactions for B22 calculations	bio	B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange	Isabell Louise Grothaus	COM POSITION DISTANCE RESTRAINT PRINT METAD COMBINE	bias colvar function vatom generic
25.023	Molecular simulations of Tau-protein oligomers	bio	metadynamics, proteins, aggregation	Giovanni Bussi	RESTART RMSD REWEIGHT_BIAS CONVERT_TO_FES FLUSH CONTACTMAP RESTRAINT PRINT METAD CUSTOM HISTOGRAM DUMPGRID	bias colvar function setup gridtools generic
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	RMSD COORDINATION OPES_METAD_EXPLORE GROUP DISTANCE MOLINFO PRINT OPES_EXPANDED COMBINE CUSTOM ENERGY CENTER GHOST ECV_MULTITHERMAL	colvar function core opes vatom generic
25.012	A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis	bio	enzyme catalysis, transition state, structure-activity relationship, free energy surface, reaction mechanism, water, alpha-amylase, sugar, QM/MM MD, OPES, committor function, machine learning	Sudip Das	UNITS POSITION BIASVALUE COORDINATION ENERGY FLUSH MATHEVAL CELL DISTANCE OPES_METAD PRINT LOAD COMBINE TORSION CUSTOM INCLUDE	bias colvar function setup opes generic
25.008	Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting	methods	metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting	Dhiman Ray	UNITS RMSD POSITION ENDPLUMED BIASVALUE GROUP DISTANCE MOLINFO OPES_METAD PRINT UPPER_WALLS METAD TORSION CUSTOM LOWER_WALLS ENERGY PYTORCH_MODEL WHOLEMOLECULES	bias pytorch colvar function setup core 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	RESTART DISTANCE PUCKERING RESTRAINT MOLINFO PRINT METAD TORSION MOVINGRESTRAINT	bias setup colvar generic
25.002	M3_PCV-ABMD	chemistry	Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor	Gian Marco Elisi	UNITS ENDPLUMED PRINT UPPER_WALLS ABMD PATHMSD	colvar generic setup bias
25.001	RNA G-quadruplex folding with ST-metaD protocol	bio	RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD	Pavlína Pokorná	ERMSD MOLINFO METAD COMBINE WHOLEMOLECULES	generic colvar function bias
24.031	DeepLNE	methods	PATHCV, OPES, OneOPES	Thorben Fröhlking	RESTART COORDINATION OPES_METAD_EXPLORE ERMSD MOLINFO PRINT OPES_EXPANDED COMBINE VOLUME ENERGY ECV_MULTITHERMAL PYTORCH_MODEL	pytorch colvar function setup opes generic
24.030	NMR guided simulation of dsRBD	bio	Metainference, NMR, protein dynamics	Debadutta Patra	STATS RDC FLUSH ALPHABETA GROUP DISTANCE MOLINFO METAINFERENCE PRINT ENSEMBLE WHOLEMOLECULES	colvar function core isdb generic multicolvar
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	RESTART COORDINATION GROUP WHOLEMOLECULES FIT_TO_TEMPLATE DISTANCE OPES_METAD PRINT CENTER UPPER_WALLS TORSION FIXEDATOM CUSTOM PATH PYTORCH_MODEL LOWER_WALLS	bias pytorch colvar function mapping setup core opes vatom 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	COMMITTOR GROUP PRINT METAD TORSION LOAD	bias colvar setup core generic
24.014	Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation	methods	data augmentation, geodesic interpolation, collective variables, protein folding	Juno Nam	RMSD COORDINATION FLUSH WHOLEMOLECULES MOLINFO DRR PRINT UPPER_WALLS METAD PYTORCH_MODEL LOWER_WALLS	pytorch bias colvar drr generic
24.011	Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble	methods	committor, machine learning	Peilin Kang	RMSD COORDINATION DISTANCE PRINT UPPER_WALLS LOWER_WALLS WHOLEMOLECULES MATHEVAL GROUP MOLINFO INCLUDE BIASVALUE ENDPLUMED TORSION UNITS POSITION ENERGY CELL LOAD CUSTOM	bias colvar function setup core generic
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	BIASVALUE MATHEVAL WHOLEMOLECULES DISTANCE PRINT UPPER_WALLS METAD CENTER LOWER_WALLS CONSTANT	bias colvar function vatom generic
23.015	MPCs aggregation	bio	opes_explore, dimerization, MPCs, self-assembly	Vikas Tiwari	COM COORDINATION OPES_METAD_EXPLORE GROUP DISTANCE PRINT UPPER_WALLS METAD CUSTOM CENTER LOWER_WALLS WHOLEMOLECULES	bias colvar function core opes vatom generic
22.041	Skipping the Replica Exchange Ladder with Normalizing Flows	methods	OPES, alanine, normalizing flows, replica exchange	Michele Invernizzi	UNITS POSITION ENDPLUMED OPES_METAD PRINT OPES_EXPANDED TORSION ENERGY ECV_MULTITHERMAL	generic setup colvar opes
22.018	Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations	bio	ligand binding, docking, EMMI, LAT1	Max Bonomi	BIASVALUE GROUP MOLINFO EMMIVOX PRINT LOAD WHOLEMOLECULES	bias setup core isdb generic
22.008	Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters	materials	Well tempered metadynamics, ab-initio, ase	Daniel Sucerquia	COM GYRATION UNITS COORDINATION FLUSH DISTANCE COORDINATIONNUMBER UPPER_WALLS METAD COMBINE LOWER_WALLS	bias colvar function setup vatom generic symfunc
21.030	Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains	bio	parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure	Jim Pfaendtner	COM GYRATION PBMETAD COORDINATION ALPHABETA DISTANCE PRINT METAD TORSION ENERGY INCLUDE	bias colvar vatom generic multicolvar
21.025	Computational and biochemical analysis of type IV pilus dynamics and stability	bio	molecular dynamics, calcium binding, Type IV pilus	Yasaman Karami	PRINT UPPER_WALLS DISTANCE LOWER_WALLS	colvar generic bias
21.008	Multi-replica biased sampling for photoisomerization processes in conjugated polymers	methods	metadynamics, FEP, replica-exchange	Adriana Pietropaolo	RESTART PBMETAD BIASVALUE MATHEVAL PRINT TORSION CONSTANT WHOLEMOLECULES	bias colvar function setup generic
21.004	Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy	bio	machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding	Dorothea Gobbo	RESTART PATHMSD PRINT UPPER_WALLS METAD LOWER_WALLS WHOLEMOLECULES	generic setup colvar bias
19.063	Protein-ligand binding through metadynamics with path CVs	bio	metadynamics, path CVs, ligand binding	Mattia Bernetti	PATHMSD PRINT UPPER_WALLS METAD LOWER_WALLS WHOLEMOLECULES	generic colvar bias
19.059	cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide	bio	bias-exchange metadynamics, cis-trans isomerization	Fabrizio Marinelli	RANDOM_EXCHANGES PRINT METAD TORSION INCLUDE	colvar generic bias
19.053	Capillary fluctuations with PLUMED	methods	nucleation, surface tension, capillary fluctuations	Gareth Tribello	UNITS MULTICOLVARDENS FOURIER_TRANSFORM GROUP MORE_THAN FCCUBIC CENTER FIND_CONTOUR_SURFACE DUMPGRID	contour function fourier setup core gridtools vatom symfunc
19.049	Determining the sizes of solid/liquid clusters in MD trajectories of nucleation	methods	nucleation, metadynamics, clustering, Steinhardt order parameters	Gareth Tribello	LOCAL_Q6 ONES CONTACT_MATRIX OUTER_PRODUCT MORE_THAN Q6 MATRIX_VECTOR_PRODUCT DFSCLUSTERING OUTPUT_CLUSTER PRINT CLUSTER_DISTRIBUTION COORDINATIONNUMBER METAD SMAC DISTANCES CLUSTER_NATOMS CUSTOM CLUSTER_PROPERTIES	bias function matrixtools adjmat clusters multicolvar generic symfunc
19.045	Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water	materials	metadynamics, well-tempered, multiple walkers, LAMMPS	Marco De La Pierre	RESTART UNITS POSITION COORDINATION GROUP FLUSH PRINT UPPER_WALLS METAD LOWER_WALLS	bias colvar setup core generic
19.042	Harmonic Linear Discriminant Analysis (HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	UNITS FLUSH DISTANCE PRINT UPPER_WALLS METAD COMBINE ENERGY	bias colvar function setup generic
19.031	Ice nucleation using PIV-based path coordinates	materials	phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics	Silvio Pipolo	PIV CELL PRINT UPPER_WALLS METAD FUNCPATHMSD LOWER_WALLS	bias colvar function generic piv
19.024	PT-MetaD-WTE	methods	metadynamics, WTE, trp cage, PT	Jim Pfaendtner	EXTERNAL COORDINATION GROUP METAD ENERGY	colvar core bias
19.018	Excited state FEP/Metadynamics simulations	chemistry	metadynamics, FEP, excited states, conjugated polymers, torsional potential	Adriana Pietropaolo	BIASVALUE MATHEVAL PRINT METAD TORSION CONSTANT WHOLEMOLECULES	colvar generic bias function
19.012	Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex	Carlo Camilloni	RMSD STATS BIASVALUE ENDPLUMED GROUP DISTANCE MOLINFO RESTRAINT PRINT UPPER_WALLS SAXS CENTER INCLUDE WHOLEMOLECULES	bias colvar function core isdb vatom generic
19.004	MI Ubiquitin	bio	metainference, NMR	Max Bonomi	RDC GROUP MOLINFO METAINFERENCE CS2BACKBONE PRINT WHOLEMOLECULES	generic core isdb

PLUMED-NEST

The public repository of the PLUMED consortium

Browse the eggs in PLUMED-NEST