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

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.
SYSTEM	System description in the free text format
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.

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

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.

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.

SYSTEM

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

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.

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