DebiChem Project
Molecular dynamics
DebiChem Molecular Dynamics

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


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DebiChem Molecular dynamics packages

Official Debian packages with high relevance
Molecular Simulator for GNUstep (GUI)
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fieldbiology, biology:structural
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works-with3dmodel, db
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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.

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 
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Ab Initio Molecular Dynamics
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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).

Molecular dynamics simulator, with building and analysis tools
Versions of package gromacs
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fieldbiology, biology:structural, chemistry
interfacecommandline, x11
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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.

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)
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Molecular Dynamics Simulator
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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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고성능 전산 화학 소프트웨어
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NWChem은 전산 화학 프로그램 패키지입니다. 대규모 과학 계산 화학 문제를 효율 적으로 처리 할 수 있는 능력과 고성능 병렬 슈퍼컴퓨터에서 기존에 워크스테이 션 클러스터까지 사용 가능한 병렬 컴퓨팅 리소스의 사용에서 확장가능한 방법을 제공합니다.

NWChem은 다음을 처리할 수 있습니다:

  • 분자의 높은 정확도의 계산을 위해 가우시안 기초 함수를 사용하는 분자 전자 구조 방법
  • 분자, 액체, 결정체, 표면, 반도체, 금속을 계산하기 위한 유사 가능성 평면파 전자 구조 방법
  • Ab-initio 및 고전 분자 역학 시뮬레이션
  • 혼합된 양자 고전 시뮬레이션
  • 수천 개 프로세서에 대한 병렬 스케일링

아래와 같은 특징을 포함합니다:

  • 분자 전자 구소 방법, 2차 도함수 분석:
  • 제한되거나/제한되지 않는 Hartree-Fock (RHF, UHF)
  • 많은 로컬, 비로컬 (그래디언트 보정) 또는 하이브리드 (로컬, 비로컬, HF) 교환 상관 관계 가능성을 사용하는 제한된 밀도 기능 이론 (DFT)
  • 분자 전자 구조 방법, 그라디언트 분석:
  • 제한된 오픈쉘 Hartree-Fock (ROHF)
  • 무제한 밀도 기능 이론 (DFT)
  • RHF 및 UHF 참조를 사용하는, 2차 Moeller-Plesset 변화 이론 (MP2)
  • ID 근사값 (RI-MP2)의 해상도를 갖는 MP2
  • 활성 공간 SCF (CASSCF) 완성
  • 시간 종속 밀도 기능 이론 (TDDFE)
  • 분자 전자 구조 방법, 단일 포인트 에너지:
  • MP2 스핀 컴포넌트 스케일링 방식 (SCS-MP2)
  • RHF 및 UHF 참조를 갖는 싱글 및 더블, 트리플 또는 pertubative 트리플 (CCSD, CCSDT, CCSD(T)) 결합 글러스터
  • 구성 상호 작용 (CISD, CISDT, CISDTQ)
  • 2차 근사 싱글 더블 결합 클러스터 (CC2)
  • 주별 다중참조 결합 클러스터 방법 (MRCC) (Brillouin-Wigner (BW-MRCC) 및 Mukherjee (Mk-MRCC) 접근법)
  • 분자 전자 구조의 더 많은 특징:
  • 전이 상태 검색, 구속 조건 및 최소 에너지 경로를 포함하는 형상 최적화 (Nudged Elastic Band (NEB) 및 Zero Temperature String 방법을 통해)
  • 진동 주파수
  • RHF, UHF, RDFT 또는 UDFT 참조를 갖는 여기상태를 위한 운동 방정식 (EOM)-CCSD,

    EOM-CCSDT, EOM-CCSD(T), CC2, 단일 배열 상호작용 (CIS), 시간종속 HF

    (TDHF) 및 TDDFT

  • 분석 구매를 포함하는, RHF, ROHF, DFT를 위한 도체와 유사한 스크리닝 모델 (COSMO)를

    사용하는 솔벤트화
    • 2 및 3 레이어 ONIOM 방법을 사용하는 하이브리드 계산
    • 스핀 궤도 위치를 통해 DFT 에 대한 스핀 프리 및 스핀 궤도 1 전자 Douglas-Kroll

      및 0차 정규 근사 (ZORA) 및 1 전자 스핀 궤도 효과를 통한 상대론적 효과 * 유사 포텐셜 평면파 전자 구조: - 분자, 액체, 결정체, 표면, 반도체 또는 금속을 계산하기 위한 유사 포텐셜 평면파

      (PSPW), Projector Augmented Wave (PAW) 또는 밴드 구조 방법 - 전환 상태 검색을 포함하는 기하/유닛 셀 최적화 - 진동 주파수 - LDA, PBE96, PBE0 교환 상관관계 가능성 (제한 및 제한되지 않음) - SIC, pert-OEP, Hartree-Fock, 및 하이브리드 기능 (제한 및 제한되지 않음) - 세미코어 교정을 갖는 Hamann, Troullier-Martins 및 Hartwigsen-Goedecker-Hutter

      평균 보존 유사 포텐셜 - 파동 함수, 밀도, 정전기 및 Wannier 플로팅 - 밴드 구조 및 상태 생성 밀도 * 제1원리 순이론 분자 역학 (CPMD): - 일정한 에너지 및 일정한 온도 역학 - 통합을 위한 Verlet 알고리즘 - 직교 좌표에 기하학 제약 조건 * 고전 분자 역학 (MD): - 단일 구성 에너지 평가 - 에너지 회소화 - 분자 역학 시뮬레이션 - 자유 에너지 시뮬레이션 (단일 및/또는 이중 토폴로지, 이중 와이드 샘플링, 및 분리 시프트 스케일링 옵션을 갖는 다단계 열역학적 섭동 (MSTP) 또는 다중설정 열역학 집적화 (MCIT) 방법) - 효과적인 쌍 전위, 1차 분극, 자가 일치 분극, 부드러운 입자 메쉬 Ewald (SPME),

      주기적인 경계 조건 및 SHAKE 제약 조건을 제공하는 Force 필드 * 혼합된 양자 고전: - 혼합된 양자 역학 및 분자 역학 (QM/MM) 최소화 및 분자 역학 시뮬레이션 - 그라디언트를 반환하는 양자 역학 방법 중에서 하나를 사용하는 양자 분자 역학 시뮬레이션.

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)
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VOTCA's coarse-graining engine
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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.

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

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

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