What is Qbics?
Qbics is a computational chemistry and biology program designed for multiscale simulations.
As chemical and biological systems grow increasingly complex, more advanced theoretical and computational methods are required. Qbics has therefore been developed to incorporate both state-of-the-art quantum mechanics (QM) and molecular mechanics (MM) methods—and, most importantly, the hybrid QM/MM approach.
All three Hamiltonians can be used for energy calculations, geometry optimizations, molecular dynamics simulations, conformational searches, and many other exciting applications!
How to Cite Qbics?
The best way to support Qbics is to cite it when it contributes to your research. Currently, please cite Qbics as follows:
- Zhang, J.; Pan, Z.; Zhao, R.; Hou, X.; Zhang, X.; Tang, Z.;Zhang, Y.; Wu, Y.; Liu, W.; Gao, J. Qbics - Quantum biology,informatics and chemistry server; Shenzhen Bay Laboratory: Shenzhen, China, 2023
How to Compile Qbics?
Click here to view the Qbics Manual.
Main Features
Qbics is under active development, and we are working hard to expand its features every day!
General
- Single precompiled executable — ready to use out of the box.
- Parallelized using OpenMP.
- Continuously adding exclusive, in-house methods
Quantum Mechanics
- Hartree-Fock (HF) and Density Functional Theory (DFT):
- Energy and gradient calculations.
- Support for LDA, GGA, meta-GGA, and hybrid functionals.
- Flexible SCF initial guess options, including fragment-based and symmetry-broken guesses.
- Built-in support for over 80 standard Gaussian basis sets and 3 pseudopotentials.
- Fully customizable user-defined basis sets and pseudopotentials.
- Target State Optimization(TSO):
- Supports arbitrary diabatic states.
- Accurately describes valence, core, double, and long-range excited states.
- Enables precise X-ray absorption spectroscopy calculations.
- Energy Decomposition Analysis(EDA):
- Applicable to both ground and excited states.
- Compatible with Generalized Kohn–Sham (GKS) and TSO frameworks.
- Wave functions are exported in .mwfn format
Molecular Mechanics
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CHARMM Force Field:
- Supports standard PDB, PSF, and CHARMM force field formats.
- Energy and gradient calculations.
- Gas-phase and periodic boundary condition (PBC) simulations.
- Electrostatics handled via cutoff and particle mesh Ewald (PME) methods.
QM/MM
- Energy and gradient calculations.
- Flexible combinations of QM and MM methods.
- Projected Hybrid Orbital (PHO) approach::
- Handles an arbitrary number of boundary covalent bonds elegantly.
- No need to manually add or remove atoms at the QM/MM interface.
- Produces reliable electronic structures.
- Implemented in a black-box manner in Qbics — easy to use with minimal setup.
Geometry Optimziation
- Supports all QM, MM, and QM/MM methods.
- Atom freezing is supported.
Molecular Dynamics
- Compatible with all QM, MM, and QM/MM methods.
- Supports NVE, NVT, and NPT ensembles.
- Enthalpy and entropy decomposition.
- Multiple restraint potentials.
- Free Energy Perturbation (FEP):
- Single- and double-topology schemes.
- Reaction coordinate support.
- Suitable for charge transfer reactions.
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Enhanced sampling:
- Built-in collective variables (e.g., bond lengths, coordination numbers).
- Custom user-defined CVs.
- Supports Metadynamics, Adaptive Biasing Force (ABF), and Extended ABF.