Summary
Molecular Dynamics
DebiChem Molecular Dynamics
This metapackage will install Molecular Dynamics packages
which might be useful for chemists.
Description
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
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DebiChem Molecular Dynamics packages
Official Debian packages with high relevance
adun.app
simulateur moléculaire pour GNUstep − interface graphique
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Versions of package adun.app |
Release | Version | Architectures |
bullseye | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 0.81-6 | amd64,armel,armhf,i386 |
stretch | 0.81-9 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.81-13 | amd64,arm64,armhf,i386 |
Debtags of package adun.app: |
field | biology, biology:structural |
interface | x11 |
role | program |
scope | application |
suite | gnustep |
uitoolkit | gnustep |
use | analysing, organizing, viewing |
works-with | 3dmodel, db |
x11 | application |
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License: DFSG free
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Adun est un simulateur bio-moléculaire qui inclut aussi une gestion des
données et des capacités d'analyse. Il a été développé au « Computational
Biophysics and Biochemistry Laboratory », qui fait partie de l'unité de
recherche sur l'informatique biomédicale de l'UPF.
Ce paquet fournit UL, le frontal graphique d'Adun.
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cp2k
Ab Initio Molecular Dynamics
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Versions of package cp2k |
Release | Version | Architectures |
jessie | 2.5.1-3 | amd64,armel,armhf,i386 |
sid | 2023.2-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
bookworm | 2023.1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 8.1-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 6.1-2 | amd64,arm64,armhf,i386 |
stretch | 4.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
upstream | 2024.3 |
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License: DFSG free
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CP2K is a program to perform simulations of solid state, liquid, molecular and
biological systems. It is especially aimed at massively parallel and linear
scaling electronic structure methods and state-of-the-art ab-initio molecular
dynamics (AIMD) simulations.
CP2K is optimized for the mixed Gaussian and Plane-Waves (GPW) method based on
pseudopotentials, but is able to run all-electron or pure plane-wave/Gaussian
calculations as well. Features include:
Ab-initio Electronic Structure Theory Methods using the QUICKSTEP module:
- Density-Functional Theory (DFT) energies and forces
- Hartree-Fock (HF) energies and forces
- Moeller-Plesset 2nd order perturbation theory (MP2) energies and forces
- Random Phase Approximation (RPA) energies
- Gas phase or Periodic boundary conditions (PBC)
- Basis sets include various standard Gaussian-Type Orbitals (GTOs), Pseudo-
potential plane-waves (PW), and a mixed Gaussian and (augmented) plane wave
approach (GPW/GAPW)
- Norm-conserving, seperable Goedecker-Teter-Hutter (GTH) and non-linear core
corrected (NLCC) pseudopotentials, or all-electron calculations
- Local Density Approximation (LDA) XC functionals including SVWN3, SVWN5,
PW92 and PADE
- Gradient-corrected (GGA) XC functionals including BLYP, BP86, PW91, PBE and
HCTH120 as well as the meta-GGA XC functional TPSS
- Hybrid XC functionals with exact Hartree-Fock Exchange (HFX) including
B3LYP, PBE0 and MCY3
- Double-hybrid XC functionals including B2PLYP and B2GPPLYP
- Additional XC functionals via LibXC
- Dispersion corrections via DFT-D2 and DFT-D3 pair-potential models
- Non-local van der Waals corrections for XC functionals including B88-vdW,
PBE-vdW and B97X-D
- DFT+U (Hubbard) correction
- Density-Fitting for DFT via Bloechl or Density Derived Atomic Point Charges
(DDAPC) charges, for HFX via Auxiliary Density Matrix Methods (ADMM) and
for MP2/RPA via Resolution-of-identity (RI)
- Sparse matrix and prescreening techniques for linear-scaling Kohn-Sham (KS)
matrix computation
- Orbital Transformation (OT) or Direct Inversion of the iterative subspace
(DIIS) self-consistent field (SCF) minimizer
- Local Resolution-of-Identity Projector Augmented Wave method (LRIGPW)
- Absolutely Localized Molecular Orbitals SCF (ALMO-SCF) energies for linear
scaling of molecular systems
- Excited states via time-dependent density-functional perturbation theory
(TDDFPT)
Ab-initio Molecular Dynamics:
- Born-Oppenheimer Molecular Dynamics (BOMD)
- Ehrenfest Molecular Dynamics (EMD)
- PS extrapolation of initial wavefunction
- Time-reversible Always Stable Predictor-Corrector (ASPC) integrator
- Approximate Car-Parrinello like Langevin Born-Oppenheimer Molecular Dynamics
(Second-Generation Car-Parrinello Molecular Dynamics (SGCP))
Mixed quantum-classical (QM/MM) simulations:
- Real-space multigrid approach for the evaluation of the Coulomb
interactions between the QM and the MM part
- Linear-scaling electrostatic coupling treating of periodic boundary
conditions
- Adaptive QM/MM
Further Features include:
- Single-point energies, geometry optimizations and frequency calculations
- Several nudged-elastic band (NEB) algorithms (B-NEB, IT-NEB, CI-NEB, D-NEB)
for minimum energy path (MEP) calculations
- Global optimization of geometries
- Solvation via the Self-Consistent Continuum Solvation (SCCS) model
- Semi-Empirical calculations including the AM1, RM1, PM3, MNDO, MNDO-d, PNNL
and PM6 parametrizations, density-functional tight-binding (DFTB) and
self-consistent-polarization tight-binding (SCP-TB), with or without
periodic boundary conditions
- Classical Molecular Dynamics (MD) simulations in microcanonical ensemble
(NVE) or canonical ensmble (NVT) with Nose-Hover and canonical sampling
through velocity rescaling (CSVR) thermostats
- Metadynamics including well-tempered Metadynamics for Free Energy
calculations
- Classical Force-Field (MM) simulations
- Monte-Carlo (MC) KS-DFT simulations
- Static (e.g. spectra) and dynamical (e.g. diffusion) properties
- ATOM code for pseudopotential generation
- Integrated molecular basis set optimization
CP2K does not implement conventional Car-Parrinello Molecular Dynamics (CPMD).
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cpptraj
fast, parallelized molecular dynamics trajectory data analysis
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Versions of package cpptraj |
Release | Version | Architectures |
trixie | 5.1.0+dfsg-4 | amd64 |
sid | 5.1.0+dfsg-4 | amd64 |
upstream | 6.4.4 |
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License: DFSG free
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CPPTRAJ is a program designed to process and analyze molecular dynamics
trajectories and relevant data sets derived from their analysis. CPPTRAJ
supports many popular MD software packages including Amber, CHARMM, Gromacs,
and NAMD.
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gromacs
Simulateur de dynamique moléculaire avec outils d'analyse et de préparation
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Versions of package gromacs |
Release | Version | Architectures |
bookworm | 2022.5-2 | amd64,arm64,mips64el,ppc64el,s390x |
jessie | 5.0.2-1 | amd64,armel,armhf,i386 |
stretch | 2016.1-2 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2019.1-1 | amd64,arm64,armhf,i386 |
bullseye | 2020.6-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2024.3-2 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
sid | 2024.4-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
Debtags of package gromacs: |
field | biology, biology:structural, chemistry |
interface | commandline, x11 |
role | program |
uitoolkit | xlib |
x11 | application |
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License: DFSG free
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GROMACS est un paquet polyvalent pour faire de la dynamique moléculaire,
comme la simulation d'équations newtoniennes du mouvement de systèmes de
millions de particules.
Il a été créé en premier lieu pour les molécules biochimiques comme les
protéines et les lipides qui ont beaucoup d'interactions covalentes
compliquées, mais comme GROMACS est extrêmement rapide pour calculer les
interactions non covalentes (qui souvent dominent les simulations),
beaucoup de groupes l'utilisent aussi pour la recherche sur des systèmes
non biologiques, comme les polymères.
Ce paquet fournit des variantes pour l’exécution sur une seule machine et
pour utiliser l’interface MPI sur plusieurs machines.
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lammps
Molecular Dynamics Simulator
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Versions of package lammps |
Release | Version | Architectures |
stretch | 0~20161109.git9806da6-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0~20181211.gitad1b1897d+dfsg1-2 | amd64,arm64,armhf,i386 |
sid | 20240207+dfsg-1.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster-backports | 20191120+dfsg1-2~bpo10+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 20210122~gita77bb+ds1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 20220106.git7586adbb6a+ds1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 0~20140523.gite5e877d-1 | amd64,armel,armhf,i386 |
stretch-backports | 0~20181211.gitad1b1897d+dfsg1-1~bpo9+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
upstream | 20240829 |
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License: DFSG free
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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.
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nwchem
??? missing short description for package nwchem :-(
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Versions of package nwchem |
Release | Version | Architectures |
sid | 7.2.3-4 | all |
jessie | 6.5+r26243-4 | amd64,armel,armhf,i386 |
buster | 6.8.1-5 | amd64,arm64,armhf,i386 |
bullseye | 7.0.2-1 | amd64,arm64,armhf,i386,mips64el,ppc64el,s390x |
bookworm | 7.0.2-4 | all |
trixie | 7.2.2-2 | all |
sid | 7.2.2-2 | all |
sid | 7.2.3-3 | all |
Debtags of package nwchem: |
field | chemistry |
role | program |
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License: DFSG free
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python3-parmed
parameter and topology file editor and molecular mechanical simulator
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Versions of package python3-parmed |
Release | Version | Architectures |
trixie | 4.2.2+dfsg-3 | amd64,arm64,ppc64el |
sid | 4.2.2+dfsg-3 | amd64,arm64,ppc64el |
bookworm | 3.4.3+dfsg-1 | amd64,arm64,ppc64el |
upstream | 4.3.0 |
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License: DFSG free
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ParmEd is a package designed to facilitate creating and easily manipulating
molecular systems that are fully described by a common classical force field.
Supported force fields include Amber, CHARMM, AMOEBA, and several others that
share a similar functional form (e.g., GROMOS).
ParmEd is capable of reading and writing to a wide array of different file
formats, like the Amber topology and coordinate files, CHARMM PSF, parameter,
topology, and coordinate files, Tinker parameter, topology, and coordinate
files, and many others. The expressive central data structure (the 'Structure'
class) makes it easy to quickly and safely manipulate a chemical system, its
underlying topology, and force field parameters describing its potential energy
function.
There are two parts of ParmEd -- a documented API that one can incorporate into
their own Python scripts and programs, and a GUI/CLI pair of programs that
provides a means to quickly perform various modifications to chemical systems
for rapid prototyping.
The API also provides bindings to the OpenMM library, permitting one to carry
out full molecular dynamics investigations using ParmEd on high-performant
hardware, like AMD and NVidia GPUs.
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python3-prody
paquet de Python pour l’analyse dynamique de protéines
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Versions of package python3-prody |
Release | Version | Architectures |
sid | 2.3.1+dfsg-3 | i386 |
sid | 2.4.1+dfsg-2 | amd64,arm64,armel,armhf,mips64el,ppc64el,riscv64 |
bookworm | 2.3.1+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
upstream | 2.5.0rc0 |
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License: DFSG free
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ProDy est un paquet de Python au code source ouvert pour l’analyse de
séquences de dynamiques et de structures de protéines. Il permet une
analyse comparative et la modélisation de dynamiques structurelles de
protéines et de co-évolutions de séquences. L’IPA rapide et flexible de
ProDy sert à une utilisation interactive ainsi qu’au développement
d’applications. ProDy est aussi fourni avec plusieurs applications
d’analyse et une interface graphique pour une analyse visuelle.
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votca
Molecular dynamics analysis - coarse-graining and charge transport
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Versions of package votca |
Release | Version | Architectures |
bookworm | 2022.1-1 | amd64,arm64,mips64el,ppc64el,s390x |
sid | 2024.1-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
trixie | 2024.1-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
upstream | 2024.2 |
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License: DFSG free
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Versatile Object-Oriented Toolkit for Coarse-Graining Applications (VOTCA)
is a modeling package for the analysis of molecular dynamics data, the
development of systematic coarse-graining techniques, and methods used for
simulating microscopic charge transport in disordered semiconductors.
Numerous molecular dynamics packages, including but not limited to
GROMACS, ESPREesSo, and LAMPPS, can be used together with VOTCA.
This package contains user programs for the coarse-graining toolkit (CSG)
and excitation transport toolkit (XTP).
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Packaging has started and developers might try the packaging code in VCS
dl-poly-classic
General purpose molecular dynamics simulation package
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Versions of package dl-poly-classic |
Release | Version | Architectures |
VCS | 1.10+dfsg-1 | all |
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License: BSD-3-Clause
Debian package not available
Version: 1.10+dfsg-1
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DL_POLY Classic is a general purpose (parallel and serial) molecular
dynamics simulation package.
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