DebiChem Molecular Dynamics packages

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.

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).

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.

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.

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.

NWChem is a computational chemistry program package. It provides methods which are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.

NWChem can handle:

• Molecular electronic structure methods using gaussian basis functions for high-accuracy calculations of molecules
• Pseudopotentials plane-wave electronic structure methods for calculating molecules, liquids, crystals, surfaces, semi-conductors or metals
• Ab-initio and classical molecular dynamics simulations
• Mixed quantum-classical simulations
• Parallel scaling to thousands of processors

Features include:

• 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.

This package provides example input scripts and depends on nwchem built for the default MPI implementation for the architecture.

The default MPI is openmpi for most debian systems. OpenMPI has known problems running nwchem over multiple nodes. If you need to compute large molecules using cluster computation, you may want to use the MPICH build provided by nwchem-mpich instead.

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.

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.

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).

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