CSG_MAP(1)

📦
version 2025.1 · 3 versions
, in debian trixie, fedora 43, fedora 44, ubuntu questing, ubuntu resolute

💅 CSG_MAP(1) — the General Commands Manual glow-up

okay bestie, welcome to the csg_map manual page, living in section 1 of the General Commands Manual, brought to you by the VOTCA Development Team. this is literally the page that tells you how to take your atomistic trajectory and make it coarse-grained. sit down, grab a strawberry 🍓, we're doing this.

✨ NAME ✨

csg_map — part of the VOTCA package 🎀

🦋 SYNOPSIS 🦋

csg_map [OPTIONS]

csg_map [--help]

that's it. that's the whole vibe check. 💖

🌸 DESCRIPTION 🌸

so what does this icon actually DO? csg_map converts a reference atomistic trajectory or configuration into a coarse-grained one, based on a mapping xml-file. that's the main character move. ✨

and here's the tea: the mapping can be applied to either an entire trajectory or a selected set of frames only (peep the options for that, bestie).

here are the example glow-ups, exactly as they appear:

  • 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, aka the whole menu. no skipping, we're listing every single one because every single one matters. 👑

  • -h, --help — display this help and exit. the classic. the escape hatch. 🚪
  • --verbose — be loud and noisy
  • --verbose1 — be very loud and noisy
  • -v, --verbose2 — be extremly loud and noisy 💀 (yes, "extremly", we keep it exactly as written, no cap)
  • --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

👑 AUTHORS 👑

Written and maintained by the VOTCA Development Team <devs@votca.org> — absolute legends, fr fr. 🫶

Copyright 2009-2024 The VOTCA Development Team (http://www.votca.org)

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

that's the legal bit and yes you do have to read it, bestie, it's giving mandatory. 📜

and that's the whole page!! this was the csg_map User Manual, coming at you from the VOTCA Development Team in the CSG_MAP(1) section of the General Commands Manual. go forth and coarse-grain, you gorgeous genius. slay. 💖✨🦋

📦 where this page comes from