DebiChem Project
Summary
Molecular dynamics
DebiChem - molekylære dynamikker

Denne metapakke vil installere molekylære dynamiske pakker, som kan være nyttige for kemikere.

Description

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DebiChem Molecular dynamics packages

Official Debian packages with high relevance

Adun.app
Molekylær simulator for GNUstep - grafisk brugerflade
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Adun er en biomolekulær simulator, som også inkluderer datahåndtering og analysemuligheder. Programmet blev udviklet ved Computational Biophysics and Biochemistry Laboratory, en del af Research Unit on Biomedical Informatics of the UPF.

Denne pakke indeholder UL, den grafiske brugerflade for Adun.

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)
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Cp2k
Ab initio-molekylærdynamik
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CP2K er et program til at udføre simuleringer af faststof-, fluid-, molekyl- samt biologiske systemer. Det er specielt rettet mod massivt parallelle og lineært skalerende elektronstrukturmetoder og simulationer med moderne ab-initio-molekylærdynamik (AIMD).

CP2K er optimeret til den blandede Gaussfunktions- og planbølgemetode (GPW) baseret på pseudopotentialer, men er også stand til at køre fuldelektron- eller rene planbølge-/Gaussfunktionsberegninger. Inkluderede funktioner:

Ab-initio elektronstrukturmetoder med QUICKSTEP-modulet:

  • Energier og kræfter fra tæthedsfunktionalteori (DFT)
  • Energier og kræfter fra Hartree-Fock (HF)
  • Energier og kræfter fra andenordens perturbationsteori med Møller-Plesset (MP2)
  • Energier med random phase approximation (RPA)
  • Periodiske eller uperiodiske (gasfase) grænsebetingelser
  • Basissæt omfatter flere standardtyper af Gaussorbitaler (GTO'er), pseudopotentialer med planbølger, »augmented« planbølger (APW) og en blandet Gaussmetode plus (»augmented«) planbølgemetode (GPW / GAPW)
  • Normkonserverende, separable Goedecker-Teter-Hutter-pseudopotentialer (GTJH) og pseudopotentialer med ikke-lineære kernekorrektioner (NLCC), eller fuldelektronberegninger
  • Lokaltæthedsapproksimationen (LDA) for XC inklusive SVWN3, SVWN5, PW92 og PADE
  • Gradientkorrigerede (GGA) XC-funktionaler inklusive BLYP, BP86, PW91, PBE og HCTH120 såvel som meta-GGA-funktionalet TPSS
  • Hybrid-XC-funktionaler med eksakt Hartree-Fockudveksling (HFX) inklusive B3LYP, PBE0 og MCY3
  • Dobbelthybridfunktionaler inklusive B2PLYP og B2GPPLYP
  • Yderligere XC-funktionaler med LibXC
  • Dispersionskorrektioner via parpotentialmodellerne DFT-D2 og DFT-D3
  • Ikke-lokale van der Waals-korrektioner for XC-funktionaler inklusive B88-vdW, PBE-vdW og B97X-D
  • DFT+U-korrektion (Hubbard)
  • Tæthedsfit for DFT via Blöchl eller tæthedsafledte atomare punktladninger (DDAPC) og HFX via »auxiliary density matrix methods« (ADMM) og for MP2/RPA via Resolution-of-identity (RI)
  • Tynde (»sparse«) matrixrepræsentationer og prescreeningteknikker for lineært skalerende udregning af Kohn-Sham-matrixelementer (KS)
  • Orbitaltransformation (OT) eller direkte inversion af det iterative underrum (DIIS) til selvkonsistent minimering (SCF)
  • Local Resolution-of-Identity Projector Augmented Wave-metode (LRIGPW)
  • Energier med absolut lokaliseret molekylorbital-SCF (ALMO-SCF) til lineært skalerende molekylsystemer
  • Exciterede tilstande via tidsafhængig tæthedsfunktionalperturbationsteori (TDDFPT)

Ab-initio-molekylærdynamik:

  • Born-Oppenheimer-molekylærdynamik (BOMD)
  • Ehrenfest-molekylærdynamik (EMD)
  • PS-ekstrapolation af begyndelsesbølgefunktion
  • Tidsreversibel altid stabil predictor-corrector-integrator (ASPC)
  • Approksimativ Car-Parrinello-agtig Born-Oppenheimer-molekylærdynamik med Langevin (Andengenerations Car-Parrinello-molekylærdynamik (SGCP))

Blandede kvante-/klassiske simulationer (QM/MM):

  • Multigrid-metoder til evaluering af Coulombvekselvirkninger mellem kvante- og klassiske dele
  • Håndtering af periodiske grænsebetingelser ved hjælp af lineært skalerende elektrostatisk kobling
  • Adaptiv QM/MM

Yderligere funktioner omfatter:

  • Enkeltpunktsenergier, geometrioptimeringer og frekvensberegninger
  • Adskillige algoritmer til nudged elastic band (NEB) til beregning af minimumenergivej (B-NEB, IT-NEB, CI-NEB, D-NEB)
  • Global optimering af geometrier.
  • Solvation via Self-Consistent Continuum Solvation-modellen (SCCS)
  • Semiempiriske beregninger med parametriseringerne AM1, RM1, PM3, MNDO, MNDO-d, PNNL og PM6, tight-binding med tæthedsfunktionalteori (DFTB) og tight-binding med selfkonsistent polarisering (SCP-TB) med valgfri periodicitet
  • Klassiske molekylærdynamiksimulationer (MD) i det mikrokanoniske ensemble (NVE) eller kanoniske ensemble (NVT) med Nose-Hoover og kanonisk sampling gennem termostater der omskalerer hastigheder (CSVR)
  • Metadynamik inklusive veltempereret metadynamik til fri energi-beregninger
  • Klassiske kraftfeltsimuleringer (MM)
  • Monte Carlo-simuleringer med Kohn-Sham-DFT
  • Statiske (f.eks. spektra) og dynamiske (f.eks. diffusion) egenskaber
  • ATOM-koden til at generere pseudopotentialer
  • Integreret optimering af molekylære basissæt

CP2K implementerer ikke konventionel Car-Parinello-molekylærdynamik (CPMD).

Gromacs
Simulator af molekyldynamik med bygge- og analyseværktøjer
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GROMACS er en alsidig pakke til at udføre molekyldynamik med, dvs. simulere Newtons bevægelsesligninger for systemer med hundrede til millioner partikler.

GROMACS er primært designet til biokemiske molekyler såsom proteiner og lipider, som har en masse komplicerede bindingsvekselvirkninger, men da GROMACS er ekstremt hurtig til at beregne ikke-bindingsvekselvirkninger (som plejer at dominere simuleringer), anvender mange grupper det også til forskning inden for ikke-biologiske systemer, f.eks. polymerer.

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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Lammps
Molekylær dynamisk simulator
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LAMMPS er en klassisk molekylær dynamisk kode, og et akronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

LAMMPS har potentiale for bløde materialer (biomolekyler, polymerer) og faste materialer (metaller, semikonduktører) og grovkornede eller mesoskopiske systemer. Programmet kan bruges til at opbygge atomer eller, mere generisk, som en parallel partikelsimulator på skalaerne atomar, meso eller kontinuum.

LAMMpS kører på enkelte processorer eller parallelt via teknikker for beskedfortolkning og en delvis-dekomponering af simuleringsdomænet. Koden er designet til at være nemt at ændre eller udvide med ny funktionalitet.

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Nwchem
Højtydende programmer til beregninger i kemi
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NWCHem er en programpakke til foretage beregninger i kemi. Den tilbyder metoder, der kan skalere i både evnen til effektiv håndtering af store problemer i videnskabelige beregninger inden for kemien, samt evnen til at gøre brug af parallelle beregningsressourcer fra højtydende parallel- supercomputere til konventionelle klynger af arbejdsstationer.

NWChem kan håndtere:

  • Molekylære, elektroniske strukturmetoder med brug af gaussisk basisfunktioner til molekylærberegninger med høj præcision
  • Elektronisk strukturmetoder til pseudopotentialer for planbølger til beregning af molekyler, væsker, krystaller, overflader, halvledere eller metaller
  • Ab-initio og klassisk simulering af molekylære dynamikker
  • Blandede, klassiske kvantum-simuleringer
  • Parallel skalering til tusinder af processorer

(Den efterfølgende beskrivelse af egenskaber bevares på engelsk).

  • 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.
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-csg
VOTCA's grovkornede motor
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VOTCA er en programpakke, som fokuserer på analyse af molekylære dynamiske data, udviklingen af systematiske grovkornede teknikker samt metoder brugt for simulering af mikroskopiske ladningstransport i fejlbehæftede semikonduktører.

Csg er Votca's grovkornede motor.

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

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