Mapping Only Mode¶
PyCGTOOL may be used in mapping only mode to simply convert an all-atom (AA) coordinate file into its coarse-grained (CG) representation.
In this respect it functions similarly to the MARTINI tool
The main uses of the functionality are:
Enable direct comparison between AA and CG simulations
Use a pre-equilibrated AA coordinate file as the starting point for a CG simulation
In order to perform the AA to CG mapping, a PyCGTOOL mapping file is required. For guidance on the creation of this file see the full tutorial.
To perform a mapping from a single snapshot file (e.g. PDB, GRO, etc.) use the command:
pycgtool <topology file> -m <MAP file>
To perform a mapping of a complete trajectory (e.g. XTC, DCD, etc.) use the command:
pycgtool <topology file> <trajectory file> -m <MAP file>