cg_spica maptraj AA_PDB AA_TRAJ CG_TRAJ [-json <jsonfile>] [-outpdb <.pdb>]
[-begin <frame>] [-last <frame>] [-nodelwat]


maptraj executes CG mapping to generate CG trajectories from AA trajectories.

This program uses MDAnalysis, a python library for analyzing MD trajectories to read and write trajectory files. Therefore, the file format of MD trajectory available in this program is the same as that can be read by this library. For installation instructions, see the official web page about MDAnalysis Installation.

The program requires a json formatted file with CG mapping information contained in the spica-tools/src directory. The option -json enables to select other json files to used for mapping. The option -begin and -last can be used to select the frames of the mapped trajectory.


cg_spica maptraj dopc.aa.pdb dopc.aa.xtc

Positional args

AA_PDB [<.pdb>]

Input all-atom configuration

AA_TRAJ [<trajectory>]

Input all-atom trajectory

CG_TRAJ [<trajectory>]

Output coarse-grained trajectory

Optional args

-outpdb <.pdb> (

Output PDB of mapped final CG configuration

-json <jsonfile> (src/spica_top.json)

Input json file for CG mapping

-begin <int> (0)

First frame in mapping

-last <int> (-1)

Last frame in mapping

-nodelwat (off)

Not delete excess CG water due to CG ion mapping