DebiChem Project
Summary
Molecular mechanics
DebiChem Molecular Mechanics

This metapackage will install Molecular Mechanics which might be useful for chemists.

The list to the right includes various software projects which are of some interest to the DebiChem Project. Currently, only a few of them are available as Debian packages. It is our goal, however, to include all software in DebiChem which can sensibly add to a high quality Debian Pure Blend.

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for DebiChem to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the DebiChem mailing list

Links to other tasks

DebiChem Molecular mechanics packages

Official Debian packages with high relevance

Adun.app
Simulador Molecular de GNUstep
Versions of package adun.app
ReleaseVersionArchitectures
squeeze0.81-4amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy0.81-5amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie0.81-6amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x
sid0.81-6amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,ppc64el,s390x
Debtags of package adun.app:
fieldbiology, biology:structural
interfacex11
roleprogram
scopeapplication
suitegnustep
uitoolkitgnustep
useanalysing, organizing, viewing
works-with3dmodel, db
x11application
Popcon: 15 users (6 upd.)*
Versions and Archs
License: DFSG free
Svn

Adun es un simulador biomolecular que además posee capacidades de gestión y análisis de datos. Ha sido desarrollado por el Laboratorio de Biofísica y Bioquímica Computacional, que forma parte de la Unidad de Investigación de Informática Biomédica de la Universidad Pompeu Fabra.

Please cite: Michael A. Johnston, Ignacio Fdez. Galván and Jordi Villà-Freixa: Framework-based design of a new all-purpose molecular simulation application: The Adun simulator. (PubMed) J. Comp. Chem. 26(15):1647-1659 (2005)
Screenshots of package adun.app
Avogadro
Molecular Graphics and Modelling System
Versions of package avogadro
ReleaseVersionArchitectures
squeeze1.0.1-3amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy1.0.3-5amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie1.0.3-10.1amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x
stretch1.0.3-10.1amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x
sid1.0.3-10.1amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,ppc64el,s390x
experimental1.1.0-4amd64,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390x
Debtags of package avogadro:
fieldchemistry
roleprogram
uitoolkitqt
useviewing
Popcon: 77 users (27 upd.)*
Versions and Archs
License: DFSG free
Svn

Avogadro is a molecular graphics and modelling system targeted at molecules and biomolecules. It can visualize properties like molecular orbitals or electrostatic potentials and features an intuitive molecular builder.

Features include:

  • Molecular modeller with automatic force-field based geometry optimization
  • Molecular Mechanics including constraints and conformer searches
  • Visualization of molecular orbitals and general isosurfaces
  • Visualization of vibrations and plotting of vibrational spectra
  • Support for crystallographic unit cells
  • Input generation for the Gaussian, GAMESS and MOLPRO quantum chemistry packages
  • Flexible plugin architecture and Python scripting

File formats Avogadro can read include PDB, XYZ, CML, CIF, Molden, as well as Gaussian, GAMESS and MOLPRO output.

Please cite: Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek and Geoffrey R Hutchison: Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. (eprint) J. Cheminf. 4:17 (2012)
Other screenshots of package avogadro
VersionURL
0.8.1-5http://screenshots.debian.net/screenshots/a/avogadro/1732_large.png
Screenshots of package avogadro
Ghemical
GNOME molecular modelling environment
Versions of package ghemical
ReleaseVersionArchitectures
squeeze2.99.2-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy3.0.0-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
stretch3.0.0-1amd64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x
sid3.0.0-1amd64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,ppc64el,s390x
Debtags of package ghemical:
fieldchemistry
interface3d, x11
roleprogram
suitegnome
uitoolkitgtk
useediting, learning, viewing
works-with3dmodel
x11application
Popcon: 30 users (11 upd.)*
Versions and Archs
License: DFSG free
Svn

Ghemical is a computational chemistry software package written in C++. It has a graphical user interface and it supports both quantum- mechanics (semi-empirical) models and molecular mechanics models. Geometry optimization, molecular dynamics and a large set of visualization tools using OpenGL are currently available.

Ghemical relies on external code to provide the quantum-mechanical calculations. Semi-empirical methods MNDO, MINDO/3, AM1 and PM3 come from the MOPAC7 package (Public Domain), and are included in the package. The MPQC package is used to provide ab initio methods: the methods based on Hartree-Fock theory are currently supported with basis sets ranging from STO-3G to 6-31G**.

Screenshots of package ghemical
Gromacs
Simulador de dinámica molecular, con herramientas de construcción y análisis
Versions of package gromacs
ReleaseVersionArchitectures
squeeze4.0.7-3amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy4.5.5-2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie5.0.2-1amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x
stretch5.0.6-1amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x
sid5.0.6-1amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,ppc64el,s390x
upstream5.1
Debtags of package gromacs:
fieldbiology, biology:structural, chemistry
interfacecommandline, x11
roleprogram
uitoolkitxlib
x11application
Popcon: 33 users (36 upd.)*
Newer upstream!
License: DFSG free
Svn

GROMACS es un paquete versátil para representar dinámica molecular. Esto es, simular las ecuaciones Newtonianas de movimiento para sistemas con cientos o incluso millones de partículas.

Está diseñado principalmente para moléculas bioquímicas como proteínas o lípidos que tienen un montón de complicadas interacciones relacionadas. Pero dado que GROMACS es extremadamente rápido calculando las interacciones no relacionadas (que normalmente dominan las simulaciones) muchos grupos también lo usan en investigaciones de sistemas no biológicos como polímeros por ejemplo.

Please cite: Berk Hess, Carsten Kutzner, David van der Spoel and Erik Lindahl: GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. (eprint) J. Chem. Theory Comput. 4(3):435-447 (2008)
Lammps
Molecular Dynamics Simulator
Versions of package lammps
ReleaseVersionArchitectures
wheezy0~20120615.gite442279-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie0~20140523.gite5e877d-1amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x
stretch0~20150313.gitfa668e1-1amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x
sid0~20150313.gitfa668e1-1amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,ppc64el,s390x
Popcon: 30 users (21 upd.)*
Versions and Archs
License: DFSG free
Git

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

Screenshots of package lammps
Votca-csg
VOTCA's coarse-graining engine
Versions of package votca-csg
ReleaseVersionArchitectures
jessie1.2.4-1amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x
stretch1.2.4-1amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x
sid1.2.4-1amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,ppc64el,s390x
Popcon: 0 users (0 upd.)*
Versions and Archs
License: DFSG free
Svn

VOTCA is a software package which focuses on the analysis of molecular dynamics data, the development of systematic coarse-graining techniques as well as methods used for simulating microscopic charge transport in disordered semiconductors.

csg is Votca's coarse-graining engine.

Please cite: Victor Ruehle, Christoph Junghans, Alexander Lukyanov, Kurt Kremer and Denis Andrienko: Versatile object-oriented toolkit for coarse-graining applications. J. Chem. Theo. Comp. 5:3211-3223 (2009)

Packaging has started and developers might try the packaging code in VCS

Vmd
presentation of traces of molecular dynamics runs
License: University_of_Illinois_non-free
Debian package not available
Svn
Version: 1.9.1-3

VMD stands for Visual Molecular Dynamics. While text books and even structure databases because of technical problems only present static pictures of proteins or DNA, for the understanding of the properties of those molecules their vibration or their movement in general is important.

The movements itself are calculated by molecular dynamics programs, such as NAMD (by the same group), Rosetta, BALLView or GROMACS. The latter two are already in the distribution, we have package build instructions for Rosetta.

VMD has a series of nice features, from displaying through animation to analysing. It can be scripted, clustered, and runs on all common OS. Its license does not allow to redistribute a Debian package. But to share these build instructions for such a package is just fine.

Please cite: W. Humphrey, A. Dalke and K. Schulten: VMD: visual molecular dynamics. (PubMed,eprint) Journal of Molecular Graphics 14(1):33-38 (1996)
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 179798