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 |
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,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 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 |
stretch | 4.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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 |
jessie | 2.5.1-3 | amd64,armel,armhf,i386 |
upstream | 2024.1 |
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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 |
sid | 5.1.0+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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
Molecular dynamics simulator, with building and analysis tools
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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 | 2024.1-1 | amd64,arm64,mips64el,ppc64el,s390x |
sid | 2024.1-1 | 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 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.
This package contains variants both for execution on a single machine, and
using the MPI interface across multiple machines.
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lammps
Molecular Dynamics Simulator
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Versions of package lammps |
Release | Version | Architectures |
bookworm | 20220106.git7586adbb6a+ds1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 20240207+dfsg-1.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,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 |
stretch | 0~20161109.git9806da6-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 20240207+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
buster | 0~20181211.gitad1b1897d+dfsg1-2 | amd64,arm64,armhf,i386 |
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 |
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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 |
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 | 7.2.2-1 | all |
sid | 7.2.2-2 | all |
Debtags of package nwchem: |
field | chemistry |
role | program |
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License: DFSG free
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NWChem은 전산 화학 프로그램 패키지입니다. 대규모 과학 계산 화학 문제를 효율적으로 처리할 수 있는 능력과 고성능 병렬 슈퍼컴퓨터에서 기존에 워크스테이션 클러스터까
지 사용 가능한 병렬 컴퓨팅 리소스의 사용에서 확장가능한 방법을 제공합니다.
NWChem이 처리할 수 있는 것:
- 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)을 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.
이 패키지는 예제 입력 스크립트를 제공하며 아키텍처에 대한 기본 MPI 구현을 위해 빌드된 nwchem에 의존합니다.
기본 MPI는 대부분 데비안 시스템을 위한 openmpi입니다. OpenMPI는 멀티 노드에 nwchem을 실행하는데 문제가 있는 것으로 알려져 있습니다. 클러스터 계산을 사용해서 대규모 분자를 계산해야 하는 경우, nwchem-mpich에서 제공하는 MPICH 빌드를 대신 사용하기를 원할 수도 있습니다.
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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 |
sid | 4.2.2+dfsg-3 | amd64,arm64,ppc64el |
bookworm | 3.4.3+dfsg-1 | amd64,arm64,ppc64el |
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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
Python package for protein dynamics analysis
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Versions of package python3-prody |
Release | Version | Architectures |
sid | 2.4.1+dfsg-2 | amd64,arm64,armel,armhf,mips64el,ppc64el,riscv64 |
sid | 2.3.1+dfsg-3 | i386 |
bookworm | 2.3.1+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
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License: DFSG free
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ProDy is a free and open-source Python package for protein structure, dynamics,
and sequence analysis. It allows for comparative analysis and modeling of
protein structural dynamics and sequence co-evolution. Fast and flexible ProDy
API is for interactive usage as well as application development. ProDy also
comes with several analysis applications and a graphical user interface for
visual analysis.
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votca
Molecular dynamics analysis - coarse-graining and charge transport
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Versions of package votca |
Release | Version | Architectures |
sid | 2024-2 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bookworm | 2022.1-1 | amd64,arm64,mips64el,ppc64el,s390x |
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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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