User input and content of README.yaml files

Each simulation in the NMRlipids databank is assigned with a README.yaml file which contains all the essential information of the simulation. These files are created from the manually contributed info.yaml files as described in Adding simulations into the NMRlipids databank. The README.yaml files are stored in the NMRlipids GitHub repository.

README.yaml files contain information that is manually entered into info.yaml files and automatically exctracted information by the AddData.py program. Table below lists the manually entered compulsory and optional parameters, as well as automatically extracted information from simulation files.

key

description

type

DOI

DOI from where the raw data is found

User given (compulsory)

TRJ

Name of the trajectory file found from DOI

TPR

Name of the topology file found from DOI

SOFTWARE

Software used to run the simulation

PREEQTIME

Pre-equilibrate time in nanoseconds.

TIMELEFTOUT

Equilibration period in the uploaded trajectory.

COMPOSITION

Molecules names and mapping files.

DIR_WRK

Temporary local working directory

UNITEDATOM_DICT

Hydrogen information for united atom simulations

TYPEOFSYSTEM

Lipid bilayer or something else

SYSTEM

System description in the free text format

PUBLICATION

Reference to a publication(s) related to the data.

User given (optional)

AUTHORS_CONTACT

Name and email of the main author(s) of the data.

BATCHID

Identifier for a series of related simulations

SOFTWARE_VERSION

Version of the used software

FF

Name of the used force field

FF_SOURCE

Source of the force field parameters

FF_DATE

Date when force field parameters were accessed

FF{molename}

Molecule specific force field information.

CPT

Name of the Gromacs checkpoint file.

LOG

Name of the Gromacs log file.

TOP

Name of the Gromacs top file.

GRO

Name of the Gromacs gro file.

EDR

Name of the Gromacs edr file.

TRAJECTORY_SIZE

Size of the trajectory file in bytes

Automatically extracted data.

TRJLENGTH

Lenght of the trajectory (ps).

TEMPERATURE

Temperature of the simulation.

NUMBER_OF_ATOMS

Number of atoms in the simulation.

DATEOFRUNNIG

Date when added into the databank

EXPERIMENT

Potentially connected experimental data

COMPOSITION

Numbers of molecules in the system

ID

Unique integer identifier of the simulation

Generated by Admin

DOI (compulsory)

Give the DOI identity for the location of simulation files. Current databank works only for the data in Zenodo, but other potential sources are may be implemented in the future. Note that the DOI must point to a specific version of dataset in Zenodo. DOIs pointing to all versions of certain dataset do not work.

TRJ (compulsory)

Give the name of the trajectory file that is found from the DOI given above.

TPR (compulsory)

Give the name of the file with topology information (tpr file in the case of Gromacs) that is found from the DOI given above.

SOFTWARE (compulsory)

Give the name of software used to run the simulation. The options are GROMACS, AMBER, NAMD, CHARMM and OPENMM. So far, only simulations run with GROMACS are accepted by the script.

PREEQTIME (compulsory)

Give the time simulated before the uploaded trajectory in nanoseconds. For example, if you upload 100-200 ns part of total 200 ns simulation, this should value should be 100.

TIMELEFTOUT (compulsory)

Give the time that should be considered as an equilibration period in the uploaded trajectory. Frames before the give time will be discarded in the analysis. For example, if you upload 0-200 ns part of total 200 ns simulation where the first 100 ns should be considered as an equilibration, this value should be 100.

COMPOSITION (compulsory)

Information about the composition (i.e., the number of molecules) of each simulation is stored in COMPOSITION as python dictionary format. As an input, the COMPOSITION requires the universal name for each molecule present in the simulation (for definitions, see Universal molecule and atom names) as the first keys. For each molecule, another dictionary containing the simulation specific residue name (NAME) and the name of the mapping file (MAPPING) needs to be then defined. Mapping file defines the universal atom names for each molecule, for details see Universal molecule and atom names). For example, the COMPOSITION dictionary input for a system containing POPC, Cholesterol (CHOL), water (SOL), sodium (SOD), and chloride (CLA) is given as:

COMPOSITION:
 CHOL:                                      # universal molecule name
  NAME: CHL1                                # simulation specific molecule name
  MAPPING: mappingCHOLESTEROLcharmm.txt     # name of the mapping file
 POPC:
  NAME: POPC
  MAPPING: mappingPOPCcharmm.txt
 SOL:
  NAME: TIP3
  MAPPING: mappingTIP3PCHARMMgui.txt
 SOD:
  NAME: SOD
  MAPPING: mappingSOD.txt
 CLA:
  NAME: CLA
  MAPPING: mappingCLA.txt

When running AddData.py, the numbers of molecules are added in additional COUNT keys into dictionaries of each molecule, see COMPOSITION (ouput) below.

DIR_WRK (compulsory)

Give the path of the working directory in your local computer. The trajectory and topology files will be downloaded to this trajectory, and temporary files created during processing will be stored here.

UNITEDATOM_DICT (compulsory for united atom trajectories)

Order parameters from united atom simulations are calculated using the buildH code. For united atom simulations, you need to tell how hydrogens are added based on definitions in the dic_lipids.py dictionary. This is done by giving a dictionary where the key is the molecule name (abbreviation listed in table above) and the value is the correct dictionary key in dic_lipids.py. If correct dictionary key is not yet found, you need to add to dic_lipids.py. In the case of an all atom simulation, UNITEDATOM is left empty.

TYPEOFSYSTEM (compulsory)

Tell whether the system is lipid bilayer or something else. Only lipid bilayers are currently supported, but other systems will be included in the future.

SYSTEM (compulsory)

Give description of system in free format. For example ‘’POPC with cholesterol at 301K’’.

PUBLICATION

Give reference to a publication(s) related to the data.

AUTHORS_CONTACT

Give the name and email of the main author(s) of the data.

BATCHID

Give an identifier for a series of related simulations e.g. NVT simulations with the same composition but different volume carried out to determine a surface pressure-area per lipid isotherm.

SOFTWARE_VERSION

Give the version of the software used.

FF

Give the name of the force field used used in the simulation.

FF_SOURCE

Describe the source of the force field parameters. For example, CHARMM-GUI, link to webpage where parameters were downloaded, or citation to a paper.

FF_DATE

Give the date when parameters were accessed or created. The format is day/month/year.

Individual force field names for molecules

In some cases special force fields are used for certain molecules. For example, non-standard parameters for ions or other molecules have been used. These can be specified giving forcefield names separately for individual molecules. These can be given as parameters named as FF+{abbreviation from table above}, i.e., FFPOPC, FFPOT, FFSOL etc.

CPT (Gromacs)

Give the name of the Gromacs checkpoint file that is found from the DOI given above. CPT stands for the name of the cpt file.

LOG (Gromacs)

Give the name of the Gromacs log file that is found from the DOI given above.

TOP (Gromacs)

Give the name of the Gromacs top file that is found from the DOI given above.

EDR (Gromacs)

Give the name of the Gromacs edr file that is found from the DOI given above.

TRAJECTORY_SIZE

Size of the trajectory file in bytes.

TRJLENGTH

Lenght of the trajectory (ps).

TEMPERATURE

Temperature of the simulation.

NUMBER_OF_ATOMS

Total number of atoms in the simulation.

DATEOFRUNNIG

Date when added into the databank.

EXPERIMENT

Potentially connected experimental data.

COMPOSITION (output)

When adding a simulation into NMRlipids databank with the AddData.py, numbers of molecules are automatically calculated and stored into COUNT keys for each molecule in the COMPOSITION dictionary. Number of lipids are calculated separately for both membrane leaflets. For example, the result for the simulation with COMPOSITION input exemplified above is:

    COMPOSITION:
     CHOL:
      NAME: CHL1
      COUNT:
       - 25
       - 25
      MAPPING: mappingCHOLESTEROLcharmm.yaml
     POPC:
      NAME: POPC
      COUNT:
       - 100
       - 100
      MAPPING: mappingPOPCcharmm.yaml
     SOL:
      NAME: TIP3
      COUNT: 9000
      MAPPING: mappingTIP3PCHARMMgui.yaml
     SOD:
      NAME: SOD
      COUNT: 21
      MAPPING: mappingSOD.yaml
     CLA:
      NAME: CLA
      COUNT: 21
      MAPPING: mappingCLA.yaml

ID

Unique numeric identifier assigned to the simulation. It is generated by the administrator of the databank.