csg_map(1) · carta

Usage

csg_map [OPTIONS]

csg_map [--help]

Overview

Convert a reference atomistic trajectory or configuration into a coarse-grained one based on a mapping xml-file. The mapping can be applied to either an entire trajectory or a selected set of frames only (see options).
* csg_map --top FA-topol.tpr --trj FA-traj.trr --out CG-traj.xtc --cg cg-map.xml
* csg_map --top FA-topol.tpr --trj FA-conf.gro --out CG-conf.gro --cg cg-map.xml
* csg_map --top FA-topol.tpr --trj FA-traj.xtc --out FA-history.dlph --no-map
* csg_map --top FA-field.dlpf --trj FA-history.dlph --out CG-history.dlph --cg cg-map.xml
* csg_map --top .dlpf --trj .dlph --out .dlph --cg cg-map.xml convert HISTORY to HISTORY_CGV

Options

Allowed options:

-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
--out arg output file for coarse-grained trajectory
--vel Write mapped velocities (if available)
--force Write mapped forces (if available)
--hybrid Create hybrid trajectory containing both atomistic
and coarse-grained
Mapping options:

--cg arg coarse graining mapping and bond definitions
(xml-file)
--map-ignore arg list of molecules to ignore separated by ;
--no-map disable mapping and act on original trajectory
Trajectory options:

--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames

Releases

6 releases since Debian 8 (Jessie); the text changed 5 times.

8
9
10
11
12
13

--cg until Debian 11 (Bullseye); --force until Debian 11 (Bullseye); --help until Debian 11 (Bullseye); --hybrid until Debian 11 (Bullseye); --map-ignore until Debian 11 (Bullseye); --nframes until Debian 11 (Bullseye); --no-map until Debian 11 (Bullseye); --out until Debian 11 (Bullseye); --top until Debian 11 (Bullseye); --trj until Debian 11 (Bullseye); --vel until Debian 11 (Bullseye); --verbose until Debian 11 (Bullseye); --verbose1 until Debian 11 (Bullseye); --verbose2 until Debian 11 (Bullseye); -h until Debian 11 (Bullseye); -v until Debian 11 (Bullseye).