DebiChem Project
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

DebiChem Molecular dynamics packages

Official Debian packages with high relevance

Adun.app
Molecular Simulator for GNUstep (GUI)
Versions of package adun.app
ReleaseVersionArchitectures
stretch0.81-9amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster0.81-13amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye0.81-14amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid0.81-14amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
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,armel,armhf,i386
Debtags of package adun.app:
fieldbiology, biology:structural
interfacex11
roleprogram
scopeapplication
suitegnustep
uitoolkitgnustep
useanalysing, organizing, viewing
works-with3dmodel, db
x11application
Popcon: 10 users (8 upd.)*
Versions and Archs
License: DFSG free
Git

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.

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)
Registry entries: OMICtools 
Screenshots of package adun.app
Cp2k
Ab Initio Molecular Dynamics
Versions of package cp2k
ReleaseVersionArchitectures
stretch4.1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster6.1-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid7.1-3amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x
wheezy2.2.426-8amd64,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie2.5.1-3amd64,armel,armhf,i386
Popcon: 16 users (9 upd.)*
Versions and Archs
License: DFSG free
Git

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)

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).

Gromacs
構築と解析ツールを含む分子動力学シミュレータ
Versions of package gromacs
ReleaseVersionArchitectures
bullseye2020.3-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster2019.1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch2016.1-2amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
squeeze4.0.7-3amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
jessie5.0.2-1amd64,armel,armhf,i386
wheezy4.5.5-2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
sid2020.3-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package gromacs:
fieldbiology, biology:structural, chemistry
interfacecommandline, x11
roleprogram
uitoolkitxlib
x11application
Popcon: 23 users (15 upd.)*
Versions and Archs
License: DFSG free
Git

GROMACS は分子動力学、つまり、数百から数百万の粒子からなるシステムについて ニュートンの運動方程式のシミュレーションを行う、多目的なパッケージです。

主に、たくさんの複雑に結合した相互作用を持つタンパク質や脂質のような生化学 分子のために設計されています。とはいえ、GROMACS は非結合性の相互作用 (通常 はそれがシミュレーションの大半を占める) の計算が極端に速いため、多くのグ ループは、たとえば高分子化合物のような、生物学以外のシステムに対する研究に も使用しています。

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)
Registry entries: Bio.tools  SciCrunch  OMICtools  Bioconda 
Lammps
Molecular Dynamics Simulator
Versions of package lammps
ReleaseVersionArchitectures
sid20200303+dfsg1-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie0~20140523.gite5e877d-1amd64,armel,armhf,i386
stretch0~20161109.git9806da6-7amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster0~20181211.gitad1b1897d+dfsg1-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye20200303+dfsg1-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
wheezy0~20120615.gite442279-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
Popcon: 20 users (9 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
Nwchem
高性能計算化学ソフトウェア
Versions of package nwchem
ReleaseVersionArchitectures
buster6.8.1-5amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye7.0.0-2amd64,arm64,armhf,i386,mips64el,ppc64el,s390x
sid7.0.0-2amd64,arm64,armhf,i386,mips64el,ppc64el,s390x
wheezy6.1-6amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie6.5+r26243-4amd64,armel,armhf,i386
Debtags of package nwchem:
fieldchemistry
roleprogram
Popcon: 9 users (7 upd.)*
Versions and Archs
License: DFSG free
Git

NWChem は計算化学プログラムパッケージです。大規模な計算化学の問題を 効率的に扱える点と、高性能並列スーパーコンピュータから従来型の ワークステーションクラスタまでの並列計算資源で利用可能であるという点に おいてスケーラブルな計算化学ツールとなることを目的としています。

NWChem ソフトウェアは次のような問題を解くことができます:

  • 分子についてのガウス基底を用いた高精度電子構造計算法
  • 分子、液体、結晶、表面、半導体、金属についての擬ポテンシャル平面基底 電子構造法
  • 第一原理および古典分子動力学シミュレーション
  • 量子・古典混合計算
  • 数千プロセッサまでスケールする並列計算

特徴一覧:

  • 分子電子構造法、解析的二次導関数
  • 制限・非制限ハートリーフォック法 (RHF/UHF)
  • 多数の局所・非局所 (勾配補正つき)・ハイブリッド (局所、非局所、HF) 交換相関ポテンシャルによる制限・非制限密度汎関数法 (DFT)
  • 分子電子構造法、解析的勾配
  • 制限開殻ハートリーフォック法 (ROHF)
  • 非制限密度汎関数法 (DFT)
  • 二次メラー・プレセット摂動法 (MP2)、RHF および UHF 参照波動関数
  • 恒等演算子分解近似 MP2 (MP2-RI)
  • 完全活性空間 SCF (CASSCF)
  • 時間依存密度汎関数法 (TDDFT)
  • 分子電子構造法、一点エネルギー計算
  • スピン成分スケール化 MP2 (SCS-MP2)
  • 結合クラスター一重・二重、三重および摂動展開三重励起 (CCSD, CCSDT, CCSD(T)) RHF および UHF参照波動関数
  • 配置間相互作用 (CISD, CISDT, CSISDTQ)
  • 二次近似結合クラスター一重・二重励起 (CC2)
  • 状態特異多参照結合クラスター法 (MRCC) (ブリュアン・ウィグナー法 (BW-MRCC) および Mukherjee法 (Mk-MRCC))
  • さらなる分子電子構造機能
  • 遷移状態探索、拘束付き最適化、最低エネルギー経路探索 (Nudged Elastic Band (NEB) 法もしくは零温度ストリング法による)を含む構造最適化
  • 振動周波数
  • RHF, ROHF, RDFT, UDFT を参照関数とする運動方程式 (EOM)-CCSD、 EOM-CCSDT、EOM-CCSD(T)、CC2、配置間相互作用一重励起 (CIS)、時間依存 HF (TDHF)による励起状態計算
  • 導体類似遮蔽モデル (COSMO) を用いた、RHF, ROHF, DFT による解析的勾配 を含む溶媒和計算
  • 二層・三層 ONIOM 法によるハイブリッド計算
  • スピンフリーおよびスピン軌道一電子 Douglas-Koll および零次正規近似 (ZORA) を通じた相対論効果補正と、スピン軌道ポテンシャルを使った DFT 向け一電子スピン軌道効果
  • 擬ポテンシャル平面波基底電子構造
  • 擬ポテンシャル平面波基底 (PSPW)、Projector Augmented Wave (PAW) 法 を用いた分子、液体、結晶、表面、半導体、金属に対するバンド構造法
  • 遷移状態探索を含む構造・単位胞最適化
  • 振動周波数
  • LDA, PBE96, PBE0 交換相関ポテンシャル (制限および非制限)
  • SIC、pert-OEP、ハートリーフォック、ハイブリッド汎関数 (制限および非制限)
  • Hamann, Troullier-Martis, Hartwigsen-Goedecker-Hutter 準内殻補正つき ノルム保存擬ポテンシャル
  • 波動関数、密度、静電、ワニエプロット
  • バンド構造と状態密度生成
  • カーパリネロ第一原理分子動力学法 (CPMD)
  • 定常エネルギーおよび定常温度動力学
  • ベルレ法による積分
  • デカルト座標系による構造拘束
  • 古典分子動力学法 (MD)
  • 単配置エネルギー評価
  • エネルギー最小化
  • 分子動力学シミュレーション
  • 自由エネルギーシミュレーション (多段熱力学的摂動法 (MSTP) もしくは 多配置熱力学的積分法 (MCTI)、単一および二重トポロジー、 二倍幅サンプリング、分離シフトスケーリングオプションつき)
  • 実行二体ポテンシャル、一次分極、自己無撞着分極、滑らかな粒子メッシュ エバルト法 (SPME)、周期的境界条件、SHAKE 拘束を提供する力場
  • 量子・古典混合
  • 量子・分子力学混合 (QM/MM) 最小化および分子動力学シミュレーション
  • 勾配を返せる全ての量子力学的手法を用いた量子分子動力学シミュレーション
Please cite: M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski, T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha, E. Apra, T.L. Windus and W.A. de Jong: NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations. Comput. Phys. Commun. 181(9):1477-1489 (2010)
Screenshots of package nwchem
Votca-csg
VOTCA's coarse-graining engine
Versions of package votca-csg
ReleaseVersionArchitectures
buster1.5-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch1.3.0-3amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie1.2.4-1amd64,armel,armhf,i386
sid1.6.2-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye1.6.2-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 1 users (4 upd.)*
Versions and Archs
License: DFSG free
Git

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

Dl-poly-classic
General purpose molecular dynamics simulation package
Versions of package dl-poly-classic
ReleaseVersionArchitectures
VCS1.10+dfsg-1all
Versions and Archs
License: BSD-3-Clause
Debian package not available
Git
Version: 1.10+dfsg-1

DL_POLY Classic is a general purpose (parallel and serial) molecular dynamics simulation package.

*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 198476