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GROMACS 2024-dev-20230525-1e2b7fd documentation

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Downloads
Release notes
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Installation guide
User guide
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- Known issues affecting users of GROMACS
- Getting started
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  - Flow Chart
- System preparation
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- Managing long simulations
- Answers to frequently asked questions (FAQs)
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- Force fields in GROMACS
- Molecular dynamics parameters (.mdp options)
- Useful mdrun features
- Getting good performance from mdrun
- Common errors when using GROMACS
- Command-line reference
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  - molecular dynamics simulation suite
  - gmx anaeig
  - gmx analyze
  - gmx angle
  - gmx awh
  - gmx bar
  - gmx bundle
  - gmx check
  - gmx chi
  - gmx cluster
  - gmx clustsize
  - gmx confrms
  - gmx convert-tpr
  - gmx convert-trj
  - gmx covar
  - gmx current
  - gmx density
  - gmx densmap
  - gmx densorder
  - gmx dielectric
  - gmx dipoles
  - gmx disre
  - gmx distance
  - gmx dos
  - gmx dssp
  - gmx dump
  - gmx dyecoupl
  - gmx editconf
  - gmx eneconv
  - gmx enemat
  - gmx energy
  - gmx extract-cluster
  - gmx filter
  - gmx freevolume
  - gmx gangle
  - gmx genconf
  - gmx genion
  - gmx genrestr
  - gmx grompp
  - gmx gyrate
  - gmx h2order
  - gmx hbond
  - gmx helix
  - gmx helixorient
  - gmx help
  - gmx hydorder
  - gmx insert-molecules
  - gmx lie
  - gmx make_edi
  - gmx make_ndx
  - gmx mdmat
  - gmx mdrun
  - gmx mindist
  - gmx mk_angndx
  - gmx msd
  - gmx nmeig
  - gmx nmens
  - gmx nmr
  - gmx nmtraj
  - gmx nonbonded-benchmark
  - gmx order
  - gmx pairdist
  - gmx pdb2gmx
  - gmx pme_error
  - gmx polystat
  - gmx potential
  - gmx principal
  - gmx rama
  - gmx rdf
  - gmx report-methods
  - gmx rms
  - gmx rmsdist
  - gmx rmsf
  - gmx rotacf
  - gmx rotmat
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  - gmx spatial
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  - gmx traj
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  - gmx vanhove
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  - Selection syntax and usage
- Terminology
- Environment Variables
- Floating point arithmetic
- Security when using GROMACS
- Policy for deprecating GROMACS functionality
Short How-To guides
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Reference Manual
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gmxapi Python package
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NBLIB API
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- Guide to Writing MD Programs
C++ API
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- Public C++ API
Developer Guide
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- Contribute to GROMACS
- Codebase overview
- Build system overview
- Change Management
- Relocatable binaries
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- Style guidelines
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- Development-time tools
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  - Using Doxygen
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  - Automation and Infrastructure
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    - GitLab CI Pipeline Execution
  - Release engineering with GitLab
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  - Source tree checker scripts
  - Automatic source code formatting
  - Unit testing
  - Physical validation
- Known issues relevant for developers
Doxygen documentation

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Deprecated functionality#

Changes anticipated to GROMACS 2024 functionality#

Functionality deprecated in GROMACS 2024#

Removed functionality

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Deprecated functionality
- Changes anticipated to GROMACS 2024 functionality
- Functionality deprecated in GROMACS 2024