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
Molecular Simulator for GNUstep (GUI)
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Versions of package adun.app |
Release | Version | Architectures |
buster | 0.81-13 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.81-6 | amd64,armel,armhf,i386 |
bullseye | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 0.81-9 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
squeeze | 0.81-4 | amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc |
wheezy | 0.81-5 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
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 is a biomolecular simulator that also includes data management and
analysis capabilities. It was developed at the Computational Biophysics
and Biochemistry Laboratory, a part of the Research Unit on Biomedical
Informatics of the UPF.
This package contains UL, the Adun GUI frontend.
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Cp2k
Ab Initio Molecular Dynamics
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Versions of package cp2k |
Release | Version | Architectures |
bullseye | 7.1-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
wheezy | 2.2.426-8 | amd64,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
jessie | 2.5.1-3 | amd64,armel,armhf,i386 |
stretch | 4.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 6.1-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 8.1-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
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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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Gromacs
Molecular dynamics simulator, with building and analysis tools
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Versions of package gromacs |
Release | Version | Architectures |
jessie | 5.0.2-1 | amd64,armel,armhf,i386 |
stretch | 2016.1-2 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
experimental | 2021~rc1-1 | amd64,arm64,armel,armhf,mipsel,ppc64el,s390x |
experimental | 2021~beta2-2 | mips64el |
sid | 2020.4-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2020.4-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2019.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
squeeze | 4.0.7-3 | amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc |
wheezy | 4.5.5-2 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
upstream | 2021~rc1 |
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 is a versatile package to perform molecular dynamics, i.e. simulate
the Newtonian equations of motion for systems with hundreds to millions of
particles.
It is primarily designed for biochemical molecules like proteins and lipids
that have a lot of complicated bonded interactions, but since GROMACS is
extremely fast at calculating the nonbonded interactions (that usually
dominate simulations) many groups are also using it for research on non-
biological systems, e.g. polymers.
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Lammps
Molecular Dynamics Simulator
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Versions of package lammps |
Release | Version | Architectures |
sid | 20200303+dfsg1-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 0~20140523.gite5e877d-1 | amd64,armel,armhf,i386 |
stretch | 0~20161109.git9806da6-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0~20181211.gitad1b1897d+dfsg1-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 20200303+dfsg1-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
wheezy | 0~20120615.gite442279-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
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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
High-performance computational chemistry software
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Versions of package nwchem |
Release | Version | Architectures |
buster | 6.8.1-5 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 6.5+r26243-4 | amd64,armel,armhf,i386 |
wheezy | 6.1-6 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
bullseye | 7.0.1-1 | amd64,arm64,armhf,i386,mips64el,ppc64el,s390x |
sid | 7.0.2-1 | amd64,arm64,armhf,i386,mips64el,ppc64el,s390x |
Debtags of package nwchem: |
field | chemistry |
role | program |
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License: DFSG free
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NWChem is a computational chemistry program package. It provides methods
which are scalable both in their ability to treat large scientific
computational chemistry problems efficiently, and in their use of available
parallel computing resources from high-performance parallel supercomputers to
conventional workstation clusters.
NWChem can handle:
- Molecular electronic structure methods using gaussian
basis functions for high-accuracy calculations of molecules
- Pseudopotentials plane-wave electronic structure methods for calculating
molecules, liquids, crystals, surfaces, semi-conductors or metals
- Ab-initio and classical molecular dynamics simulations
- Mixed quantum-classical simulations
- Parallel scaling to thousands of processors
Features include:
- Molecular electronic structure methods, analytic second derivatives:
- Restricted/unrestricted Hartree-Fock (RHF, UHF)
- Restricted Density Functional Theory (DFT) using many local,
non-local (gradient-corrected) or hybrid (local, non-local, and HF)
exchange-correlation potentials
- Molecular electronic structure methods, analytic gradients:
- Restricted open-shell Hartree-Fock (ROHF)
- Unrestricted Density Functional Theory (DFT)
- Second-order Moeller-Plesset perturbation theory (MP2), using RHF and UHF
reference
- MP2 with resolution of the identity approximation (RI-MP2)
- Complete active space SCF (CASSCF)
- Time-Dependent Density Functional Theory (TDDFT)
- Molecular electronic structure methods, single-point energies:
- MP2 spin-component scaled approach (SCS-MP2)
- Coupled cluster singles and doubles, triples or pertubative triples
(CCSD, CCSDT, CCSD(T)), with RHF and UHF reference
- Configuration interaction (CISD, CISDT, and CISDTQ)
- Second-order approximate coupled-cluster singles doubles (CC2)
- State-specific multireference coupled cluster methods (MRCC)
(Brillouin-Wigner (BW-MRCC) and Mukherjee (Mk-MRCC) approaches)
- Further molecular electronic structure features:
- Geometry optimization including transition state searches, constraints
and minimum energy paths (via the Nudged Elastic Band (NEB) and Zero
Temperature String methods)
- Vibrational frequencies
- Equation-of-motion (EOM)-CCSD, EOM-CCSDT, EOM-CCSD(T), CC2,
Configuration-Interaction singles (CIS), time-dependent HF (TDHF) and
TDDFT, for excited states with RHF, UHF, RDFT, or UDFT reference
- Solvatisation using the Conductor-like screening model (COSMO) for RHF,
ROHF and DFT, including analytical gradients
- Hybrid calculations using the two- and three-layer ONIOM method
- Relativistic effects via spin-free and spin-orbit one-electron
Douglas-Kroll and zeroth-order regular approximations (ZORA) and
one-electron spin-orbit effects for DFT via spin-orbit potentials
- Pseudopotential plane-wave electronic structure:
- Pseudopotential Plane-Wave (PSPW), Projector Augmented Wave (PAW) or band
structure methods for calculating molecules, liquids, crystals, surfaces,
semi-conductors or metals
- Geometry/unit cell optimization including transition state searches
- Vibrational frequencies
- LDA, PBE96, and PBE0 exchange-correlation potentials (restricted and
unrestricted)
- SIC, pert-OEP, Hartree-Fock, and hybrid functionals (restricted and
unrestricted)
- Hamann, Troullier-Martins and Hartwigsen-Goedecker-Hutter norm-conserving
pseudopotentials with semicore corrections
- Wavefunction, density, electrostatic and Wannier plotting
- Band structure and density of states generation
- Car-Parrinello ab-initio molecular dynamics (CPMD):
- Constant energy and constant temperature dynamics
- Verlet algorithm for integration
- Geometry constraints in cartesian coordinates
- Classical molecular dynamics (MD):
- Single configuration energy evaluation
- Energy minimization
- Molecular dynamics simulation
- Free energy simulation (multistep thermodynamic perturbation (MSTP) or
multiconfiguration thermodynamic integration (MCTI) methods with options
of single and/or dual topologies, double wide sampling, and separation-
shifted scaling)
- Force fields providing effective pair potentials, first order
polarization, self consistent polarization, smooth particle mesh Ewald
(SPME), periodic boundary conditions and SHAKE constraints
- Mixed quantum-classical:
- Mixed quantum-mechanics and molecular-mechanics (QM/MM) minimizations and
molecular dynamics simulations
- Quantum molecular dynamics simulation by using any of the quantum
mechanical methods capable of returning gradients.
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Votca-csg
VOTCA's coarse-graining engine
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Versions of package votca-csg |
Release | Version | Architectures |
buster | 1.5-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.3.0-3 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.2.4-1 | amd64,armel,armhf,i386 |
sid | 1.6.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.6.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 1.6.4 |
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License: DFSG free
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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.
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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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