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file_types:
# GROMACS
- type: tpr
  engine: gromacs
  category: run input
  source: https://manual.gromacs.org/current/reference-manual/file-formats.html
- type: gro
  engine: gromacs
  category: structure
  source: https://manual.gromacs.org/current/reference-manual/file-formats.html
- type: mdp
  engine: gromacs
  category: parameter
  source: https://manual.gromacs.org/current/reference-manual/file-formats.html
- type: itp
  engine: gromacs
  category: topology
  source: https://manual.gromacs.org/current/reference-manual/file-formats.html
- type: ndx
  engine: gromacs
  category: topology
- type: top
  engine: gromacs
  category: topology
  source: https://manual.gromacs.org/current/reference-manual/file-formats.html
- type: xtc
  engine: gromacs
  category: trajectory
  source: https://manual.gromacs.org/current/reference-manual/file-formats.html
- type: trr
  engine: gromacs
  category: trajectory
  source: https://manual.gromacs.org/current/reference-manual/file-formats.html
- type: edr
  engine: gromacs
  category: energy
  source: https://manual.gromacs.org/current/reference-manual/file-formats.html
- type: tng
  engine: gromacs
  category: trajectory
  source: https://manual.gromacs.org/current/reference-manual/file-formats.html
- type: cpt
  engine: gromacs
  category: others
- type: log
  engine: gromacs
  category: others
  source: https://manual.gromacs.org/current/reference-manual/file-formats.html
# NAMD
- type: conf
  engine: namd
  category: parameter
  source: https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node26.html
- type: namd
  engine: namd
  category: parameter
  source: https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node26.html  
- type: psf
  engine: namd
  category: topology
  source: https://www.melbournebioinformatics.org.au/tutorials/tutorials/molecular_dynamics_201/molecular_dynamics_201/
- type: inp
  engine: namd
  category: topology
- type: prm
  engine: namd
  category: topology
- type: crd
  engine: namd
  category: coordinate
  source: https://userguide.mdanalysis.org/stable/formats/reference/crd.html#crd-format
- type: dcd
  engine: namd
  category: trajectory
  source: https://userguide.mdanalysis.org/stable/formats/reference/dcd.html#dcd-format
- type: coor
  engine: namd
  category: coordinate
- type: vel
  engine: namd
  category: trajectory
- type: xsc
  engine: namd
  category: topology
# AMBER
- type: prep
  engine: amber
  category: parameter
  source: http://amber.manchester.ac.uk/index.html
- type: frcmod
  engine: amber
  category: parameter
  source: https://tsiangsun.github.io/programming/Amber-setup-prmtop-inpdrd/
- type: prmtop
  engine: amber
  category: topology
  source: https://userguide.mdanalysis.org/stable/formats/reference/top.html
- type: parm7
  engine: amber
  category: topology
  source: https://userguide.mdanalysis.org/stable/formats/reference/top.html
- type: rst7
  engine: amber
  category: coordinate
  source: https://ambermd.org/tutorials/advanced/tutorial21/section1.htm
- type: inpcrd
  engine: amber
  category: trajectory
  source: https://tsiangsun.github.io/programming/Amber-setup-prmtop-inpdrd/
- type: mdcrd
  engine: amber
  category: trajectory
  source: https://tsiangsun.github.io/programming/Amber-setup-prmtop-inpdrd/
- type: mdout
  engine: amber
  category: none
  source: https://tsiangsun.github.io/programming/Amber-setup-prmtop-inpdrd/
- type: nc
  engine: amber
  category: trajectory
- type: ncdf
  engine: amber
  category: trajectory
- type: trj
  engine: amber
  category: trajectory
- type: leap
  engine: amber
  category: none
  source: Amber 2017 Reference Manual, http://ambermd.org/doc12/Amber17.pdf
- type: ptraj
  engine: amber
  category: none
  source: http://archive.ambermd.org/201601/0233.html
# CHARMM
- type: psf
  engine: charmm
  category: topology
  source: https://userguide.mdanalysis.org/stable/formats/reference/psf.html#psf-format
- type: crd
  engine: charmm
  category: coordinate
  source: https://userguide.mdanalysis.org/stable/formats/reference/crd.html#crd-format
- type: rst
  engine: charmm
  category: restart
- type: dcd
  engine: charmm
  category: trajectory
  source: https://userguide.mdanalysis.org/stable/formats/reference/dcd.html#dcd-format
# MISC
- type: params
  engine: unknown
  category: none
  source: https://figshare.com/articles/dataset/Molecular_dynamics_simulation_of_radiation_damage_cascades_in_diamond_Dataset_1_/11876313
# DESMOND
- type: cms
  engine: desmond
  category: coordinate
  source: Desmond 2.2 User Manual, https://www.cines.fr/wp-content/uploads/2014/01/des22_user_manual.pdf
- type: cpt
  engine: desmond
  category: checkpoint
  source: Desmond 2.2 User Manual, https://www.cines.fr/wp-content/uploads/2014/01/des22_user_manual.pdf
- type: csb
  engine: desmond
  category: topology
  source: Desmond 2.2 User Manual, https://www.cines.fr/wp-content/uploads/2014/01/des22_user_manual.pdf
- type: dms
  engine: desmond
  category: coordinate
  source: https://www.psc.edu/resources/anton/anton-2-covid/
- type: dtr
  engine: desmond
  category: trajectory
  source: Desmond 2.2 User Manual, https://www.cines.fr/wp-content/uploads/2014/01/des22_user_manual.pdf