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Biomolecular Simulation Database

BioSimDB

BioSim Deposition

This form automatically extracts useful data that describes a molecular dynamics simulation. Whenever you share your data, include this metadata with the simulation files to make your data more findable, accessible, interoperable and reuseable (FAIR).

Instructions:
  • To extract simulation metadata, please upload a topology and corresponding trajectory file/s.
  • Multiple trajectory files can be uploaded with a single associated topology file, both file types are required.
  • Various simulation file formats are accepted and read using MDAnalysis, please ensure your files are compatible.
  • This form uses the biosim-schema to define and group biosim metadata. Missing terms or units? Please consider raising an issue or contributing to the schema.
  • Automatically add metadata associated with each entry using the "Extract metadata" button.
  • Please fill in any missing metadata fields manually where applicable, click on each field name for further information about data field requirements.
  • Two options are available for your extracted simulation metadata:
    1. Download the simulation metadata as a json file and share alongside simulation files.
    2. Submit your simulation files and metadata in one step to BioSimDB, you will be directed to a login page and asked to authorize this application. Please continue and complete the data submission process in BioSimDB.
  • Clear all fields when uploading new files, as manually filled in fields are preserved unless cleared.
Any Problems?
  • This deposition form is in active development, with new features being added, there may be a few bugs 🐞 that have crept in!
  • If you experience any errors or warnings when using this form, please report them here.

Setup

Setup Tool

Minimisation

Energy Tolerance
Minimisation Distance Step Size
Minimisation Algorithm Use Cmd/Ctrl to select multiple options.
Simulation Tool Use Cmd/Ctrl to select multiple options.
Simulation Software Use Cmd/Ctrl to select multiple options.
Number Of Minimisation Steps

Equilibration

Simulation Tool Use Cmd/Ctrl to select multiple options.
Simulation Software Use Cmd/Ctrl to select multiple options.

Production

Simulation Tool Use Cmd/Ctrl to select multiple options.
Simulation Software Use Cmd/Ctrl to select multiple options.
Simulation Method Use Cmd/Ctrl to select multiple options.
Simulation Software Version Extracted from files

Analysis

Analysis Tool Use Cmd/Ctrl to select multiple options.
Analysis Software Use Cmd/Ctrl to select multiple options.
Analysis Method Use Cmd/Ctrl to select multiple options.

Ensemble

Ensemble Type
Random Seed

Integrator

Frame Step
Integration Step
Simulation Time
Integrator Algorithm
Number Of Steps

Barostat

Compressibility
Compressibility Vector
Target Pressure
Target Pressure Vector
Pressure Time Constant
Pressure Coupling Frequency
Barostat Algorithm
Pressure Coupling Type

Thermostat

Target Temperature
Target Temperature Vector
Collision Frequency
Temperature Time Constant
Friction Coefficient
Thermostat Algorithm
Coupling Group
Chain Length

Interactions

Restraints?
Electrostatic Cutoff Distance
Vdw Cutoff Distance
Bond Length Constraints Algorithm
Long Range Interaction Method

Simulation Averages

Average Kinetic Energy
Average Potential Energy
Average Enthalpy
Average Pressure
Average Temperature
Average Volume
Average Volume Vector

Connectivity

Bonds?
Dihedrals?

Particles

Masses?
Fixed Charges?
Coarse Grained?
System Charge
Resolution

Simulation Box

Box Dimensions
Box Angles
Box Type
Periodic Boundary Conditions

Trajectory Output

Positions?
Forces?
Velocities?
Polarizable Charges?
Energies?
Water?
Replica?
Frame Count

System Counts

Salt Concentration
Total Molecule Count
Total Atom Count
Unique Molecule Count

Molecule ID 1

Predicted Structure?
Modified?
Molecular Weight
Molecule Charge
PDB ID
UNIPROT ID
SMILES
InChI
InChIKey
AlphaFold ID
PubChem CID
Molecular Formula
Molecule Count
Atom Count
Monomer Count
Simulated Particle Names
Simulated Molecule Name
Protein Sequence
Nucleic Sequence

Water Potential

Modified?
Water Potential Name

Protein Potential

Modified?
Protein Potential Name

Lipid Potential

Modified?
Lipid Potential Name

Nucleic Potential

Modified?
Nucleic Potential Name

Carbohydrate Potential

Modified?
Carbohydrate Potential Name

Polymer Potential

Modified?
Polymer Potential Name

General Potential

Modified?
General Potential Name

Machine Learned Potential

Modified?
Machine Learned Potential Name

Hardware

Memory Per Node
Execution Platform
Node Type
CPU Vendor
CPU Architecture
GPU Vendor
Node Count
Sockets Per Node
Cores Per Socket
Threads Per Core
GPUs Per Node

Software

Operating System
Scheduler
MPI Library
Container Runtime

Performance

Wall Time
Energy Consumption