Information to be stored in the databank dictionary files

To speed up the analysis of the trajectories in the NMRlipids IVb project, we will build a beta version of NMRlipids databank containing the trajectories related to this project. For this, and for the future, we need to decide which information will be stored in the dictionary files that compose the databank. Beta version of the databank builder code is here and the databank itself is here.

Currently the plan is to have the following information in the dictionary:

Given by the user

DOI="10.5281/zenodo.3474862"        # DOI link to the data (required)
MAPPING= MappingFilePath             # correct mapping file for the simulation (required)

@SOFTWARE=gromacs                    # name of the used software (required)
@FF=CHARMM36                              # name of the used force field (required)
@TRJ=traj_comp.xtc                           # name of the trajectory file  (required)
@TPR=mdrun.tpr                                # name of the tpr (or corresponding) file  (required)

@SYSTEM=POPC_303K                   # free text name given by user
@FF_SOURCE=CHARMM-GUI         # source of the used force field
@FF_DATE=??                                   # date of the force field
@INI=md_in.gro                                  # name of the gro (or corresponding) file   

PREeqTIME=PreEqTime                    # length of trajectory simulated before uploaded part

@POPC=POPC                                 # names of the molecules used in the simulation, if not default
@POPG=POPG
@POPS=POPS
@POPE=POPE
@POT=POT
@SOD=SOD
@CLA=CLA
@CAL=CAL
@TIP3=TIP3

Read and stored automatically


TRAJECTORY_LENGTH=LengthOfTraj  # length of uploaded trajectory in ns
@TEMPERATURE=0                              # simulation temperature

@NPOPCu=0                                          # number of lipid molecules in upper leaflet
@NPOPGu=0
@NPOPSu=0
@NPOPEu=0

@NPOPCl=0                                           # number of lipid molecules in lower leaflet
@NPOPGl=0
@NPOPSl=0
@NPOPEl=0

@NPOT=0                                               # number of other molecules
@NSOD=0
@NCLA=0
@NCAL=0
@NTIP3=0

The values with "(required)" in the end of the comment are compulsory information.

The length of the trajectory, pre-equilibration times, and separate number of lipids in each leaflet are added based on the suggestions in the online meeting.

This type of dictionary contains minimum amount of information and it should be possible to extend it some point if needed. Any comments or opinions about this are welcomed.

NMRLipids / NMRlipidsIVPEandPG

Information to be stored in the databank dictionary files #16