{ "$schema": "http://json-schema.org/draft-07/schema#", "$id": "https://gmd.ceitec.cz/schema/GROMACS-2025-1.schema.json", "title": "GROMACS Simulation Schema", "description": "This schema defines the structure of metadata and parameters used in a GROMACS simulation environment.", "properties": { "administrative": { "properties": { "title": { "title": "Title of the dataset", "type": "string" }, "creator": { "description": "ORCIDs are encouraged", "title": "Creator of the dataset or data curator", "type": "string" }, "publishing_institution": { "description": "Institution that published the dataset. Use the ROR ID (https://ror.org/) if available", "title": "Publishing Institution", "type": "string" }, "publication_year": { "title": "Publication Year", "type": "integer" }, "identifier": { "description": "DOI or other identifier", "title": "Identifier", "type": "string" }, "software_information": { "type": "object", "title": "Software Information", "description": "Details of the software environment used to perform the simulation.", "properties": { "software": { "type": "string", "title": "Software Name", "description": "Name of the molecular dynamics package (e.g., 'GROMACS')." }, "version": { "type": "string", "title": "Software Version", "description": "Version of the software used (e.g., '2023.1')." } } } }, "type": "object" }, "simulated_object": { "properties": { "protein_id": { "title": "Protein Identification", "description": "Enter either the PDB ID or the Uniprot ID, more than one protein can be entered", "type": "array", "items": { "type": "object", "properties": { "type": { "title": "Identifier Source", "type": "string", "enum": ["PDB ID", "Uniprot ID"] }, "identifier": { "title": "Structure ID", "type": "string" } }, "required": ["type", "identifier"] } }, "ligand_id": { "title": "Ligand Identification", "description": "Enter a ligand identifier from a recognized database", "type": "array", "items": { "type": "object", "properties": { "type": { "title": "Identifier Source", "type": "string", "enum": [ "PDB Ligand ID", "PubChem CID", "ChEMBL ID", "DrugBank ID", "ZINC ID", "HMDB ID", "KEGG Compound ID" ] }, "identifier": { "title": "Ligand ID", "type": "string" } }, "required": ["type", "identifier"] } }, "solvent": { "type": "object", "properties": { "type": { "title": "Solvent Type", "type": "string", "enum": ["Water", "Water and Ions", "Water and Organic Solvent", "Other"] }, "name": { "title": "Solvent Name", "type": "string" }, "concentration": { "title": "Solvent Concentration", "description": "Concentration of the solvent in the simulation box in mol/L", "type": "number" } } } }, "type": "object" }, "simulation": { "type": "object", "title": "Simulation Level Data", "description": "Contains GROMACS simulation parameters (mdp fields), including force fields and input records.", "properties": { "forcefield": { "type": "string", "title": "Force Field", "description": "Specifies the force field used for the simulation (e.g., 'AMBER99SB', 'CHARMM36', etc.)." }, "filename": { "type": "string", "title": "Filename", "description": "A reference to the primary GROMACS input or configuration file name." }, "inputrec": { "type": "object", "title": "MDP Input Record", "description": "Collection of GROMACS parameters typically found in an .mdp file.", "properties": { "integrator": { "type": "string", "title": "Integrator", "description": "Defines the type of integrator (e.g., 'md', 'sd', 'md-vv', etc.)." }, "tinit": { "type": "number", "title": "Initial Time", "description": "Sets the starting time (in ps) of the simulation." }, "dt": { "type": "number", "title": "Time Step", "description": "Integration time step in picoseconds." }, "nsteps": { "type": "integer", "title": "Number of Steps", "description": "Total number of simulation steps to perform." }, "init-step": { "type": "integer", "title": "Initial Step", "description": "Index of the initial step (allows continuation runs)." }, "simulation-part": { "type": "integer", "title": "Simulation Part", "description": "Helps GROMACS handle continuation runs by labeling parts of the simulation." }, "mts": { "type": "string", "title": "MTS", "description": "Specifies multi-time stepping parameters if used." }, "mass-repartition-factor": { "type": "number", "title": "Mass Repartition Factor", "description": "Factor used when repartitioning masses in a simulation." }, "comm-mode": { "type": "string", "title": "Center of Mass Communication Mode", "description": "Method for removing center of mass motion (e.g., 'Linear', 'Angular')." }, "nstcomm": { "type": "integer", "title": "COM Removal Frequency", "description": "Frequency to remove center of mass motion in steps." }, "bd-fric": { "type": "number", "title": "Brownian Dynamics Friction", "description": "Used when integrator is BD; friction constant." }, "ld-seed": { "type": "integer", "title": "Random Seed for LD/SD", "description": "Seed for the random number generator used in Langevin/Brownian dynamics." }, "emtol": { "type": "number", "title": "Energy Minimization Tolerance", "description": "Convergence criterion for energy minimization." }, "emstep": { "type": "number", "title": "EM Step Size", "description": "Step size in energy minimization." }, "niter": { "type": "integer", "title": "Number of Iterations", "description": "Used for certain iterative algorithms in energy minimization." }, "fcstep": { "type": "integer", "title": "Force Constant Step", "description": "Step for the force constant in energy minimization cycles." }, "nstcgsteep": { "type": "integer", "title": "Conjugate Gradient Frequency", "description": "Steps between CG updates in steepest descent minimization." }, "nbfgscorr": { "type": "integer", "title": "Number of BFGS Corrections", "description": "Used by BFGS minimization to set the maximum number of corrections." }, "rtpi": { "type": "number", "title": "Time between rtp calculations", "description": "Useful parameter in integrator algorithms controlling certain updates." }, "nstxout": { "type": "integer", "title": "Position Output Frequency", "description": "Frequency in steps for writing coordinates to trajectory." }, "nstvout": { "type": "integer", "title": "Velocity Output Frequency", "description": "Frequency in steps for writing velocities to trajectory." }, "nstfout": { "type": "integer", "title": "Force Output Frequency", "description": "Frequency in steps for writing forces to trajectory." }, "nstlog": { "type": "integer", "title": "Log Output Frequency", "description": "Frequency in steps for writing to the GROMACS log file." }, "nstcalcenergy": { "type": "integer", "title": "Energy Calculation Frequency", "description": "Frequency in steps for calculation of energies." }, "nstenergy": { "type": "integer", "title": "Energy Output Frequency", "description": "Frequency in steps for writing energies to the energy file." }, "nstxout-compressed": { "type": "integer", "title": "Compressed Trajectory Output Frequency", "description": "Frequency in steps for writing compressed coordinates (xtc)." }, "compressed-x-precision": { "type": "integer", "title": "Compressed X Precision", "description": "Precision in bits for compressed trajectories." }, "cutoff-scheme": { "type": "string", "title": "Cutoff Scheme", "description": "Method for calculating non-bonded interactions (e.g., 'Verlet', 'group')." }, "nstlist": { "type": "integer", "title": "Neighbor List Update Frequency", "description": "Number of steps between construction of the neighbor list." }, "pbc": { "type": "string", "title": "Periodic Boundary Conditions", "description": "Dimension(s) along which periodic boundary conditions are applied." }, "periodic-molecules": { "type": "string", "title": "Periodic Molecules", "description": "Whether molecules are treated as periodic objects." }, "verlet-buffer-tolerance": { "type": "number", "title": "Verlet Buffer Tolerance", "description": "Controls size of the buffered pair list in Verlet scheme." }, "verlet-buffer-pressure-tolerance": { "type": "number", "title": "Verlet Buffer Pressure Tolerance", "description": "Allows for a dynamic pair-list resizing under pressure coupling." }, "rlist": { "type": "number", "title": "Neighbor List Cutoff", "description": "Cutoff for the neighbor list in nm." }, "coulombtype": { "type": "string", "title": "Coulomb Type", "description": "Treatment of long-range electrostatics (e.g., 'PME', 'Reaction-Field', 'Cut-off')." }, "coulomb-modifier": { "type": "string", "title": "Coulomb Modifier", "description": "Modifier for the Coulomb potential (e.g., 'Potential-shift')." }, "rcoulomb-switch": { "type": "number", "title": "Coulomb Switch Distance", "description": "Distance at which the Coulomb potential begins switching." }, "rcoulomb": { "type": "number", "title": "Coulomb Cutoff", "description": "Distance at which the Coulomb potential is truncated or switched." }, "epsilon-r": { "type": "number", "title": "Dielectric Constant", "description": "Relative dielectric constant of the medium." }, "epsilon-rf": { "type": "string", "title": "Reaction-Field Dielectric", "description": "Value of the dielectric constant used for reaction-field calculations." }, "vdw-type": { "type": "string", "title": "van der Waals Type", "description": "Method for treating van der Waals interactions (e.g., 'Cut-off', 'Shift')." }, "vdw-modifier": { "type": "string", "title": "van der Waals Modifier", "description": "Modifier for the vdw potential (e.g., 'Potential-shift')." }, "rvdw-switch": { "type": "number", "title": "VdW Switch Distance", "description": "Distance at which the van der Waals potential starts to switch." }, "rvdw": { "type": "number", "title": "VdW Cutoff", "description": "Distance at which the van der Waals potential is truncated or switched." }, "DispCorr": { "type": "string", "title": "Dispersion Correction", "description": "Choice of dispersion correction (e.g., 'EnerPres', 'No')." }, "table-extension": { "type": "number", "title": "Table Extension", "description": "Extension of lookup tables beyond the cutoff for custom interactions." }, "fourierspacing": { "type": "number", "title": "Fourier Spacing", "description": "Grid spacing for PME in nm." }, "fourier-nx": { "type": "integer", "title": "PME Grid Points (X)", "description": "Number of x-direction grid points for PME." }, "fourier-ny": { "type": "integer", "title": "PME Grid Points (Y)", "description": "Number of y-direction grid points for PME." }, "fourier-nz": { "type": "integer", "title": "PME Grid Points (Z)", "description": "Number of z-direction grid points for PME." }, "pme-order": { "type": "integer", "title": "PME Interpolation Order", "description": "Order of the interpolation for PME (e.g., 4)." }, "ewald-rtol": { "type": "number", "title": "Ewald Tolerance", "description": "Accuracy tolerance for Ewald summation or PME." }, "ewald-rtol-lj": { "type": "number", "title": "Ewald Tolerance (LJ)", "description": "Accuracy tolerance for LJ-PME or Ewald correction for LJ." }, "lj-pme-comb-rule": { "type": "string", "title": "LJ PME Combination Rule", "description": "Defines how combining rules for LJ interactions are handled under PME." }, "ewald-geometry": { "type": "string", "title": "Ewald Geometry", "description": "Geometry used for Ewald summation (e.g., '3d', '3dc')." }, "epsilon-surface": { "type": "number", "title": "Surface Dielectric Constant", "description": "Effective dielectric at the surface for Ewald-based methods." }, "ensemble-temperature-setting": { "type": "string", "title": "Temperature Setting", "description": "Description of how temperature is controlled (e.g., 'Berendsen', 'Nose-Hoover')." }, "ensemble-temperature": { "type": "number", "title": "Ensemble Temperature", "description": "Target temperature for the system in Kelvin." }, "tcoupl": { "type": "string", "title": "Temperature Coupling", "description": "Temperature coupling algorithm (e.g., 'V-rescale', 'Nose-Hoover')." }, "nsttcouple": { "type": "integer", "title": "Temp. Coupling Frequency", "description": "Number of steps between temperature coupling updates." }, "nh-chain-length": { "type": "integer", "title": "Nose-Hoover Chain Length", "description": "Number of thermostats in the Nose-Hoover chain." }, "print-nose-hoover-chain-variables": { "type": "string", "title": "Print NH Chain Variables", "description": "If 'yes', prints Nose-Hoover chain variables in the log." }, "pcoupl": { "type": "string", "title": "Pressure Coupling", "description": "Pressure coupling algorithm (e.g., 'Berendsen', 'Parrinello-Rahman')." }, "pcoupltype": { "type": "string", "title": "Pressure Coupling Type", "description": "Defines isotropic, semi-isotropic, or anisotropic coupling." }, "nstpcouple": { "type": "integer", "title": "Pressure Coupling Frequency", "description": "Number of steps between pressure coupling updates." }, "tau-p": { "type": "number", "title": "Pressure Time Constant", "description": "Coupling time constant for pressure regulation." }, "compressibility (3x3)": { "type": "array", "title": "Compressibility Matrix", "description": "3x3 matrix describing compressibility for each dimension.", "items": { "type": "array", "items": { "type": "number" }, "minItems": 3, "maxItems": 3 }, "minItems": 3, "maxItems": 3 }, "ref-p (3x3)": { "type": "array", "title": "Reference Pressure Matrix", "description": "3x3 matrix specifying reference pressure(s) in each dimension.", "items": { "type": "array", "items": { "type": "number" }, "minItems": 3, "maxItems": 3 }, "minItems": 3, "maxItems": 3 }, "refcoord-scaling": { "type": "string", "title": "Reference Coordinate Scaling", "description": "Determines how coordinates are scaled under pressure coupling." }, "posres-coms": { "type": "array", "title": "Position Restraints (Coms)", "description": "3-element array for controlling positions via center of mass restraints.", "items": { "type": "number" }, "minItems": 3, "maxItems": 3 }, "posres-comBs": { "type": "array", "title": "Position Restraints (ComBs)", "description": "3-element array for controlling positions of another group via center of mass restraints.", "items": { "type": "number" }, "minItems": 3, "maxItems": 3 }, "QMMM": { "type": "string", "title": "QMMM", "description": "Flag indicating quantum mechanics/molecular mechanics approach usage." } } }, "qm-opts": { "type": "object", "title": "Quantum Mechanics Options", "description": "Additional parameters for QM or hybrid QM/MM simulations in GROMACS.", "properties": { "ngQM": { "type": "integer", "title": "Number of QM Groups", "description": "Defines how many groups are treated quantum mechanically." }, "constraint-algorithm": { "type": "string", "title": "Constraint Algorithm", "description": "Algorithm for constraints (e.g., 'LINCS', 'SHAKE')." }, "continuation": { "type": "string", "title": "Continuation Run", "description": "Specifies if this run is a continuation from a previous simulation." }, "Shake-SOR": { "type": "string", "title": "Shake-SOR", "description": "Option to use successive over-relaxation with SHAKE constraints." }, "shake-tol": { "type": "number", "title": "Shake Tolerance", "description": "Tolerance level for the SHAKE algorithm." }, "lincs-order": { "type": "integer", "title": "LINCS Order", "description": "Expansion order used in the LINCS constraint algorithm." }, "lincs-iter": { "type": "integer", "title": "LINCS Iterations", "description": "Number of iterative correction steps in LINCS." }, "lincs-warnangle": { "type": "number", "title": "LINCS Warning Angle", "description": "Threshold angle for issuing LINCS warnings." }, "nwall": { "type": "integer", "title": "Number of Walls", "description": "Controls the inclusion of walls in the simulation box." }, "wall-type": { "type": "string", "title": "Wall Type", "description": "Defines the wall potential type." }, "wall-r-linpot": { "type": "number", "title": "Wall Linear Pot. Radius", "description": "Distance threshold for linearization in wall potential." }, "wall-atomtype[0]": { "type": "integer", "title": "Wall Atom Type 0", "description": "Atom type used to represent wall 0." }, "wall-atomtype[1]": { "type": "integer", "title": "Wall Atom Type 1", "description": "Atom type used to represent wall 1." }, "wall-density[0]": { "type": "number", "title": "Wall Density 0", "description": "Density of wall 0." }, "wall-density[1]": { "type": "number", "title": "Wall Density 1", "description": "Density of wall 1." }, "wall-ewald-zfac": { "type": "number", "title": "Wall Ewald Z-Factor", "description": "Factor used in Ewald summation for walls." }, "pull": { "type": "string", "title": "Pull Code", "description": "Option to activate pulling simulations (umbrella sampling, steered MD, etc.)." }, "awh": { "type": "string", "title": "AWH", "description": "Activated weight histogram method for free energy calculations." }, "rotation": { "type": "string", "title": "Rotation", "description": "Allows rotating constraints or biasing in free energy calculations." }, "interactiveMD": { "type": "string", "title": "Interactive MD", "description": "Specifies if the simulation is run in interactive mode." }, "disre": { "type": "string", "title": "Distance Restraints", "description": "Controls whether distance restraints are used." }, "disre-weighting": { "type": "string", "title": "Distance Restraints Weighting", "description": "Describes how distance restraints are weighted." }, "disre-mixed": { "type": "string", "title": "Distance Restraints Mixed", "description": "Combines multiple distance restraints in a single potential if set." }, "dr-fc": { "type": "number", "title": "Distance Restraint Force Constant", "description": "Force constant used for distance restraints." }, "dr-tau": { "type": "number", "title": "Distance Restraint Time Constant", "description": "Time constant for exponential averaging in distance restraints." }, "nstdisreout": { "type": "integer", "title": "Distance Restraint Output Frequency", "description": "Number of steps between writing distance restraint data." }, "orire-fc": { "type": "number", "title": "Orientation Restraint Force Constant", "description": "Force constant for orientation restraints." }, "orire-tau": { "type": "number", "title": "Orientation Restraint Time Constant", "description": "Time constant for orientation restraint averaging." }, "nstorireout": { "type": "integer", "title": "Orientation Restraint Output Frequency", "description": "Number of steps between writing orientation restraint data." }, "free-energy": { "type": "string", "title": "Free Energy", "description": "Controls free-energy perturbation or expanded ensemble simulations." }, "cos-acceleration": { "type": "number", "title": "Acceleration in Cosine Space", "description": "Used in certain advanced sampling or nonequilibrium methods." }, "deform (3x3)": { "type": "array", "title": "Deformation Matrix (3x3)", "description": "3x3 matrix for deforming the simulation box over time.", "items": { "type": "array", "items": { "type": "number" }, "minItems": 3, "maxItems": 3 }, "minItems": 3, "maxItems": 3 }, "simulated-tempering": { "type": "string", "title": "Simulated Tempering", "description": "Flag and parameters for simulated tempering method." }, "swapcoords": { "type": "string", "title": "Swap Coordinates", "description": "Coordinates can be swapped between replicas in REMD or other advanced methods." }, "userint1": { "type": "integer", "title": "User Integer 1", "description": "Custom user-defined integer parameter 1." }, "userint2": { "type": "integer", "title": "User Integer 2", "description": "Custom user-defined integer parameter 2." }, "userint3": { "type": "integer", "title": "User Integer 3", "description": "Custom user-defined integer parameter 3." }, "userint4": { "type": "integer", "title": "User Integer 4", "description": "Custom user-defined integer parameter 4." }, "userreal1": { "type": "number", "title": "User Real 1", "description": "Custom user-defined floating-point parameter 1." }, "userreal2": { "type": "number", "title": "User Real 2", "description": "Custom user-defined floating-point parameter 2." }, "userreal3": { "type": "number", "title": "User Real 3", "description": "Custom user-defined floating-point parameter 3." }, "userreal4": { "type": "number", "title": "User Real 4", "description": "Custom user-defined floating-point parameter 4." }, "applied-forces": { "type": "object", "title": "Applied Forces Section", "description": "Contains sub-sections for external/applied forces such as electric fields or density-guided simulations.", "properties": { "electric-field": { "type": "object", "title": "Electric Field", "description": "Definition of applied electric fields in x, y, z directions.", "properties": { "x": { "type": "object", "title": "Electric Field (X)", "description": "Parameters for the electric field along the X axis.", "properties": { "E0": { "type": "string", "title": "Amplitude", "description": "Field amplitude or magnitude." }, "omega": { "type": "string", "title": "Angular Frequency", "description": "Frequency for oscillatory electric fields." }, "t0": { "type": "string", "title": "Start Time", "description": "Time at which the field is turned on." }, "sigma": { "type": "string", "title": "Width Parameter", "description": "Used if the field has a Gaussian or other shape in time." } } }, "y": { "type": "object", "title": "Electric Field (Y)", "description": "Parameters for the electric field along the Y axis.", "properties": { "E0": { "type": "string", "title": "Amplitude", "description": "Field amplitude or magnitude." }, "omega": { "type": "string", "title": "Angular Frequency", "description": "Frequency for oscillatory electric fields." }, "t0": { "type": "string", "title": "Start Time", "description": "Time at which the field is turned on." }, "sigma": { "type": "string", "title": "Width Parameter", "description": "Used if the field has a Gaussian or other shape in time." } } }, "z": { "type": "object", "title": "Electric Field (Z)", "description": "Parameters for the electric field along the Z axis.", "properties": { "E0": { "type": "string", "title": "Amplitude", "description": "Field amplitude or magnitude." }, "omega": { "type": "string", "title": "Angular Frequency", "description": "Frequency for oscillatory electric fields." }, "t0": { "type": "string", "title": "Start Time", "description": "Time at which the field is turned on." }, "sigma": { "type": "string", "title": "Width Parameter", "description": "Used if the field has a Gaussian or other shape in time." } } } } }, "density-guided-simulation": { "type": "object", "title": "Density Guided Simulation", "description": "Enables and configures density-guided MD with specified reference density.", "properties": { "active": { "type": "string", "title": "Active", "description": "Turns density-guided simulation on or off." }, "group": { "type": "string", "title": "Atom Group", "description": "Specifies the group of atoms or molecules for density guidance." }, "similarity-measure": { "type": "string", "title": "Similarity Measure", "description": "Metric used for comparing current and reference densities." }, "atom-spreading-weight": { "type": "string", "title": "Atom Spreading Weight", "description": "Weight distribution function for atoms in the density grid." }, "force-constant": { "type": "string", "title": "Force Constant", "description": "Defines the strength of the restraining force based on density." }, "gaussian-transform-spreading-width": { "type": "string", "title": "Spreading Width", "description": "Width of the Gaussian spread used to construct the density map." }, "gaussian-transform-spreading-range-in-multiples-of-width": { "type": "string", "title": "Spreading Range", "description": "Extent of the spread around each atom in multiples of the width." }, "reference-density-filename": { "type": "string", "title": "Reference Density Filename", "description": "Path to the file holding the reference density distribution." }, "nst": { "type": "string", "title": "Update Frequency", "description": "Frequency (in steps) at which the density force is updated." }, "normalize-densities": { "type": "string", "title": "Normalize Densities", "description": "Whether to normalize both reference and current densities before comparison." }, "adaptive-force-scaling": { "type": "string", "title": "Adaptive Force Scaling", "description": "Option to scale the restraining force adaptively." }, "adaptive-force-scaling-time-constant": { "type": "string", "title": "Adaptive Scaling Time Constant", "description": "Time constant for adjusting the adaptive force scale." }, "shift-vector": { "type": "string", "title": "Shift Vector", "description": "Vector to shift the reference density in space." }, "transformation-matrix": { "type": "string", "title": "Transformation Matrix", "description": "Matrix to rotate or scale the reference density." } } }, "qmmm-cp2k": { "type": "object", "title": "QM/MM CP2K Interface", "description": "Controls the QM/MM interface if using CP2K as the QM engine.", "properties": { "active": { "type": "string", "title": "Active", "description": "Turns the QM/MM CP2K interface on or off." }, "qmgroup": { "type": "string", "title": "QM Group", "description": "Specifies which group of atoms is treated quantum mechanically." }, "qmmethod": { "type": "string", "title": "QM Method", "description": "The quantum mechanical method or basis set used (in CP2K terms)." }, "qmfilenames": { "type": "string", "title": "QM Filenames", "description": "Paths or patterns for files needed by CP2K (input, etc.)." }, "qmcharge": { "type": "string", "title": "QM Charge", "description": "Net charge of the QM region." }, "qmmultiplicity": { "type": "string", "title": "QM Multiplicity", "description": "Spin multiplicity of the QM system." } } }, "colvars": { "type": "object", "title": "Collective Variables Module", "description": "Interface to a colvars-like module for advanced sampling (e.g., NAMD colvars).", "properties": { "active": { "type": "string", "title": "Active", "description": "Turns the colvars module on or off." }, "configfile": { "type": "string", "title": "Configuration File", "description": "Specifies the external configuration file for colvars." }, "seed": { "type": "string", "title": "Random Seed", "description": "Seed for any stochastic processes within colvars." } } } } } } }, "grpopts": { "type": "object", "title": "Group Options", "description": "Options for temperature groups and coupling settings.", "properties": { "nrdf": { "type": "array", "title": "Number of Degrees of Freedom (Groups)", "description": "Defines the degrees of freedom per temperature group.", "items": { "type": "number" }, "minItems": 2, "maxItems": 2 }, "ref-t": { "type": "array", "title": "Reference Temperature (Groups)", "description": "Target temperature for each group in Kelvin.", "items": { "type": "number" }, "minItems": 2, "maxItems": 2 }, "tau-t": { "type": "array", "title": "Temperature Coupling Time Constants", "description": "Time constants for temperature coupling of each group in ps.", "items": { "type": "number" }, "minItems": 2, "maxItems": 2 } } }, "annealing": { "type": "array", "title": "Annealing Method (Groups)", "description": "Defines annealing method (e.g., 'single', 'periodic') for temperature groups.", "items": { "type": "string" }, "minItems": 2, "maxItems": 2 }, "annealing-npoints": { "type": "array", "title": "Number of Annealing Points", "description": "Defines how many points are used for each group's annealing schedule.", "items": { "type": "integer" }, "minItems": 2, "maxItems": 2 }, "acc": { "type": "array", "title": "Acceleration for Groups", "description": "Acceleration (in nm/ps^2) applied to different groups along x, y, z directions.", "items": { "type": "number" }, "minItems": 3, "maxItems": 3 }, "nfreeze": { "type": "array", "title": "Freeze Groups", "description": "Specifies whether (and how) certain groups are frozen in x, y, z directions.", "items": { "type": "string" }, "minItems": 3, "maxItems": 3 }, "energygrp-flags": { "type": "array", "title": "Energy Group Flags", "description": "Specifies which energy terms to store or print for certain groups.", "items": { "type": "array", "items": { "type": "integer" }, "minItems": 1, "maxItems": 1 }, "minItems": 1, "maxItems": 1 }, "header": { "type": "object", "title": "Run Header", "description": "General header information for the simulation run.", "properties": { "bIr": { "type": "string", "title": "IR Data Flag", "description": "Indicates presence of an input record for reading." }, "bBox": { "type": "string", "title": "Box Flag", "description": "Indicates presence of box dimension data." }, "bTop": { "type": "string", "title": "Topology Flag", "description": "Indicates presence of topology data." }, "bX": { "type": "string", "title": "Coordinates Flag", "description": "Indicates presence of coordinate data." }, "bV": { "type": "string", "title": "Velocity Flag", "description": "Indicates presence of velocity data." }, "bF": { "type": "string", "title": "Force Flag", "description": "Indicates presence of force data." }, "natoms": { "type": "integer", "title": "Number of Atoms", "description": "Total number of atoms in the simulation." }, "lambda": { "type": "string", "title": "Lambda", "description": "Coupling parameter for free energy calculations or scaling interactions." }, "buffer size": { "type": "integer", "title": "Buffer Size", "description": "Size of buffer used for storing coordinate/velocity/force data." } } }, "box (3x3)": { "type": "array", "title": "Box Matrix (3x3)", "description": "Simulation box vectors in a 3x3 matrix.", "items": { "type": "array", "items": { "type": "number" }, "minItems": 3, "maxItems": 3 }, "minItems": 3, "maxItems": 3 }, "box_rel (3x3)": { "type": "array", "title": "Relative Box Matrix (3x3)", "description": "Box vectors relative to some reference, if used.", "items": { "type": "array", "items": { "type": "number" }, "minItems": 3, "maxItems": 3 }, "minItems": 3, "maxItems": 3 }, "boxv (3x3)": { "type": "array", "title": "Box Velocity (3x3)", "description": "Time derivatives of box vectors if the box is changing in time.", "items": { "type": "array", "items": { "type": "number" }, "minItems": 3, "maxItems": 3 }, "minItems": 3, "maxItems": 3 }, "pres_prev (3x3)": { "type": "array", "title": "Previous Pressure Tensor (3x3)", "description": "Pressure tensor from the previous step, stored for coupling continuity.", "items": { "type": "array", "items": { "type": "number" }, "minItems": 3, "maxItems": 3 }, "minItems": 3, "maxItems": 3 }, "svir_prev (3x3)": { "type": "array", "title": "Previous Virial (3x3)", "description": "Virial tensor from the previous step, used in pressure calculations.", "items": { "type": "array", "items": { "type": "number" }, "minItems": 3, "maxItems": 3 }, "minItems": 3, "maxItems": 3 }, "fvir_prev (3x3)": { "type": "array", "title": "Previous Full Virial (3x3)", "description": "Full virial tensor from the previous step, used for continuity in coupling.", "items": { "type": "array", "items": { "type": "number" }, "minItems": 3, "maxItems": 3 }, "minItems": 3, "maxItems": 3 }, "nosehoover_xi": { "type": "string", "title": "Nose-Hoover Xi", "description": "Variable associated with the Nose-Hoover thermostat chain." }, "Group statistics": { "type": "object", "title": "Group Statistics", "description": "Records of how many atoms belong to each relevant group used in the simulation.", "properties": { "T-Coupling": { "type": "object", "title": "Temperature Coupling Group", "description": "Statistics about the group used for temperature coupling.", "properties": { "atoms": { "type": "array", "title": "Atom Indices", "description": "List of atom indices in this group.", "items": { "type": "integer" }, "minItems": 2, "maxItems": 2 }, "total atoms": { "type": "integer", "title": "Total Atoms in Group", "description": "Number of atoms belonging to this temperature coupling group." } } }, "Energy Mon.": { "type": "object", "title": "Energy Monitor Group", "description": "Group used for energy monitoring or additional output.", "properties": { "atoms": { "type": "array", "title": "Atom Indices", "description": "List of atom indices in this group.", "items": { "type": "integer" }, "minItems": 1, "maxItems": 1 }, "total atoms": { "type": "integer", "title": "Total Atoms in Group", "description": "Number of atoms belonging to this group." } } }, "Acc. not used": { "type": "object", "title": "Acceleration Not Used", "description": "Statistics for the group not subjected to acceleration.", "properties": { "atoms": { "type": "array", "title": "Atom Indices", "description": "List of atom indices in this group.", "items": { "type": "integer" }, "minItems": 1, "maxItems": 1 }, "total atoms": { "type": "integer", "title": "Total Atoms in Group", "description": "Number of atoms in the group that does not use acceleration." } } }, "Freeze": { "type": "object", "title": "Freeze Group", "description": "Group of atoms that are frozen in some or all dimensions.", "properties": { "atoms": { "type": "array", "title": "Atom Indices", "description": "List of atom indices in this group.", "items": { "type": "integer" }, "minItems": 1, "maxItems": 1 }, "total atoms": { "type": "integer", "title": "Total Atoms in Group", "description": "Number of frozen atoms in the group." } } }, "User1": { "type": "object", "title": "User Group 1", "description": "Custom user-defined group 1 for specialized statistics or manipulations.", "properties": { "atoms": { "type": "array", "title": "Atom Indices", "description": "List of atom indices in this user group.", "items": { "type": "integer" }, "minItems": 1, "maxItems": 1 }, "total atoms": { "type": "integer", "title": "Total Atoms in Group", "description": "Number of atoms in this user-defined group." } } }, "User2": { "type": "object", "title": "User Group 2", "description": "Custom user-defined group 2 for specialized statistics or manipulations.", "properties": { "atoms": { "type": "array", "title": "Atom Indices", "description": "List of atom indices in this user group.", "items": { "type": "integer" }, "minItems": 1, "maxItems": 1 }, "total atoms": { "type": "integer", "title": "Total Atoms in Group", "description": "Number of atoms in this user-defined group." } } }, "VCM": { "type": "object", "title": "Center of Mass Group", "description": "Group used to handle or remove center of mass motion.", "properties": { "atoms": { "type": "array", "title": "Atom Indices", "description": "List of atom indices in this group.", "items": { "type": "integer" }, "minItems": 1, "maxItems": 1 }, "total atoms": { "type": "integer", "title": "Total Atoms in Group", "description": "Number of atoms used for center of mass calculations in this group." } } }, "Compressed X": { "type": "object", "title": "Compressed Coordinates Group", "description": "Specifies the group for which compressed coordinates might be written.", "properties": { "atoms": { "type": "array", "title": "Atom Indices", "description": "List of atom indices in this group.", "items": { "type": "integer" }, "minItems": 1, "maxItems": 1 }, "total atoms": { "type": "integer", "title": "Total Atoms in Group", "description": "Number of atoms whose coordinates may be compressed." } } }, "Or. Res. Fit": { "type": "object", "title": "Orientational Restraint Fit Group", "description": "Group of atoms used for orientation restraint fitting or alignment.", "properties": { "atoms": { "type": "array", "title": "Atom Indices", "description": "List of atom indices in this group.", "items": { "type": "integer" }, "minItems": 1, "maxItems": 1 }, "total atoms": { "type": "integer", "title": "Total Atoms in Group", "description": "Number of atoms used for orientation restraints or RMSD fitting." } } }, "QMMM": { "type": "object", "title": "QM/MM Group", "description": "Group of atoms under QM treatment in hybrid simulations.", "properties": { "atoms": { "type": "array", "title": "Atom Indices", "description": "List of atom indices in this QM/MM group.", "items": { "type": "integer" }, "minItems": 1, "maxItems": 1 }, "total atoms": { "type": "integer", "title": "Total Atoms in Group", "description": "Number of atoms in the QM/MM group." } } } } } } }, "system": { "type": "object", "title": "System Level Data", "description": "Describes the overall system setup, such as water model and box dimensions.", "properties": { "water_model": { "type": "string", "title": "Water Model", "description": "The water model used in the simulation (e.g., 'TIP3P', 'SPC/E')." }, "box_size_and_shape": { "type": "array", "title": "Box Dimensions", "description": "Size of the simulation box in x, y, z dimensions (in nm).", "items": { "type": "number" }, "minItems": 3, "maxItems": 3 } } } } }