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To reference or cite the objects present in the Software Heritage archive, permalinks based on SoftWare Hash IDentifiers (SWHIDs) must be used.
Select below a type of object currently browsed in order to display its associated SWHID and permalink.

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Citations

This interface enables to generate software citations, provided that the root directory of browsed objects contains a citation.cff or codemeta.json file.
Select below a type of object currently browsed in order to generate citations for them.

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Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
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

Software Heritage — Copyright (C) 2015–2025, The Software Heritage developers. License: GNU AGPLv3+.
The source code of Software Heritage itself is available on our development forge.
The source code files archived by Software Heritage are available under their own copyright and licenses.
Terms of use: Archive access, API— Contact— JavaScript license information— Web API

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