What is Qbics?

Qbics is a computational chemistry and biology program for multiscale simulations. More advanced theoretical and computational methods are demanded as systems interested in chemical and biological studies are becoming increasingly complicated. Therefore, Qbics has been developed to contain both state-of-the-art quantum mechanics (QM) and molecular mechanics (MM) method, and more importantly, QM/MM approach. All the 3 Hamiltonians can be used to perform energy calculations, geometry optimizations, molecular dynamic simulations, conformation searches, and many fantastic things!

How to Cite Qbics?

How to Compile Qbics?

Click here to the Qbics Manual.

Main Features

Qbics is being actively developed. We are working hard to make this list of features longer everyday!

General

• Just a single precompiled executable, so can be used "out-of-box".
• Parallelization: OpenMP.
• Many exclusive methods are adding to Qbics.

Quantum Mechanics

• Hartree-Fock (HF) and density functional theory (DFT):
  • Energy and gradient calculations.
  • LDA, GGA, meta GGA and hybrid functionals.
  • Flexible initial guess (fragment, symmetry broken) for SCF.
  • More than 80 standard Gaussian basis sets and 3 pseudopotentials.
  • Self-defined basis sets and pseudopotentals.
• Target state optimization (TSO):
  • Arbitrary diabtic states.
  • Accurate valence, core, double, and long-range excited states.
  • Accurate X-ray absorption spectroscopy.
• Energy decomposition analysis (EDA):
  • Ground and excited states.
  • Generalized Kohn-Sham (GKS) and TSO schemes.
• Wave functions are output in mwfn format.

Molecular Mechanics

• CHARMM force field:
  • Accept standard PDB, PSF and CHARMM force field formats.
  • Energy and gradient calculations.
  • Gas phase and periodic boundary condition (PBC).
  • Cutoff and partical mesh Ewald (PME) scheme for electrostatic interactions.

QM/MM

• Energy and gradient calculations.
• Arbitrary combinations of QM and MM methods.
• Projected hybrid orbital (PHO):
  • Can tread arbitrary number of boundary covalent bonds in an elegant way: no manually adding or removing atoms are needed.
  • Reasonable electronic structures can be obtained.
  • In Qbics, PHO is implemented in a black-box way, meaning that it is highly easy to use.

Geometry Optimziation

• All QM, MM, and QM/MM methods can be used.
• Frozen atoms are supported.

Molecular Dynamics

• All QM, MM, and QM/MM methods can be used.
• NVE, NVT, and NPT ensembles.
• Enthalpy and entropy separation.
• Several restraint potentials.
• Free energy perturbation (FEP):
  • Single- and double-topology.
  • Reaction coordinates.
  • Charge transfer reactions.
• Enhanced sampling:
  • Default (like bond length, coordination numbers) and self-defined collective variables (CV).
  • Metadynamics, adaptive biased force (ABF), and extended ABF.