GromacsTopology(inpMagiC=None, system=None, topfile='topol.top', geometry=None, **kwargs)

Creates GROMACS topology file *.top for the system.

The system can be directly provided as a parameter, read from magic.inp file, or initiated from list of molecular types and number of corresponding molecules. For two latter cases *.mcm-files shall be present in the same directory. Number of molecules in the resulting system should be manually checked once the top-file is created.

inpMagiC (str)

: Input file for MagiC.Core, used to define system's composition, i.e. list of moleculartypes and number of molecules of each type

system (system)

: the system topology to export

geometry (str)

: File with the starting geometry of the system in xmol format. If provided a corresponding .gro-file will be generated

topfile (str)

: File to write the topology. Default 'topol.top'

dfset (DFset)

: Set of potentials/RDFs having SameAsBond-records. If provided, the topology will take into account SameAsBond records from the DFset

These two parameters only required if the system to be directly composed from mcm-files

mcmfile

: List of mcm-files defining molecular types

NMolMType

: List of number of molecules of each type

Examples:

[fontsize=\small]
MT.GromacsTopology('magic.inp', geometry='start.xmol')
MT.GromacsTopology(system=system, geometry='start.xmol')
MT.GromacsTopology(system=system, mcmfile=['DMPC.CG', 'Chol.CG'],  NMolMType=[30, 30]))