DebiChem Project
Summary
Semi empirical calculations
DebiChem Semi Empirical

This metapackage will install Semi Empirical which might be useful for chemists.

Description

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DebiChem Semi empirical calculations packages

Official Debian packages with high relevance

Cp2k
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).

Molds
Semi-empirical electronic structure and molecular dynamics
Versions of package molds
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jessie0.3.1-1amd64,armhf,i386
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buster0.3.1-1amd64,arm64,armhf,i386,mips64el,ppc64el,s390x
bullseye0.3.1-1amd64,arm64,armhf,i386,mips64el,ppc64el,s390x
bookworm0.3.1-1amd64,arm64,armhf,i386,mips64el,ppc64el,s390x
sid0.3.1-1amd64,arm64,armhf,i386,mips64el,ppc64el,s390x
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MolDS is a semi-empirical electronic structure and molecular dynamics package.

Features includes:

  • Semi-Empirical methods CNDO2, INDO, ZINDO/S, MNDO, AM1 and PM3
  • Excited States via Single Configuration Interaction (CIS)
  • Dispersion corrections to AM1 (AM1-D) and PM3 (PM3-D)
  • Pairwise Distance Directed Gaussian (PDDG) correction to PM3 (PM3/PDDG)
  • Single-Point, geometry optimization, Molecular Dynamics (MD), Monte-Carlo (MC) and Polymer Molecular Dynamics (RPMD) type of calculations

MolDS currently ships parameters for the elements H, C, N, O, and S.

Mopac
Molecular Orbital PACkage (MOPAC)
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MOPAC is a general-purpose semiempirical molecular orbital package for the study of solid state and molecular structures and reactions.

The semiempirical Hamiltonians MNDO, AM1, PM3, PM6, RM1, MNDO-d and PM7 are used in the electronic part of the calculation to obtain molecular orbitals, the heat of formation and its derivative with respect to molecular geometry.

Using these results MOPAC calculates the vibrational spectra, thermodynamic quantities, isotopic substitution effects and force constants for molecules, radicals, ions, and polymers. For studying chemical reactions, a transition state location routine and two transition state optimizing routines are available. For users to get the most out of the program, they must understand how the program works, how to enter data, how to interpret the results, and what to do when things go wrong.

Mopac7-bin
Semi-empirical Quantum Chemistry Library (binaries)
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fieldchemistry
roleprogram
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MOPAC provides routines to solve the electronic structure of molecules on a semi-empirical level. Available methods include MNDO, MINDO/3, AM1 and PM3.

This package contains the MOPAC7 binaries.

Xtb
semiempirical extended tight-binding program package
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xtb program performs semiempirical quantummechanical calculations. The underlying effective Hamiltonian is derived from density functional tight binding (DFTB). This implementation of the xTB Hamiltonian is currently compatible with the zeroth, first and second level parametrisation for geometries, frequencies and non-covalent interactions (GFN) as well as with the ionisation potential and electron affinity (IPEA) parametrisation of the GFN1 Hamiltonian. The generalized born (GB) model with solvent accessable surface area (SASA) is also available available in this version. Ground state calculations for the simplified Tamm-Danceoff approximation (sTDA) with the vTB model are currently not implemented.

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