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
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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 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。
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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
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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 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
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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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