Computational Chemistry
Useful Techniques
- Energy Units and Conversion using FORTRAN
- Gaussian: BSSE calculation
- Gaussian: Calculate Single-Point Energy using SAC-CI method
- Gaussian: Extract XYZ Coordinate from Output file
- Gaussian: Finding the Transition State of Chemical Reaction
- Gaussian: How to Compute Bond Energy and Bond Order using NBO
- Gaussian: Start to Practice Computational Chemistry
- LAMMPS: Strategy for Molecular Dynamics Simulation
- Molpro: Calculate Stationary Energy
- NWChem: Constrained DFT module
- ORCA: DLPNO-CCSD(T) Calculation
- ORCA: Get Started with ORCA
Molecular Visualizations
- Gaussview: Creating Electron density on Electrostatic Potential
- gOpenmol: Visualization of Electron Density & PES
- VMD: Render High Resolution Image of Isodensity Surface with Electrostatic Potential
- VMD: Render image using Tachyon Renderer
Tips and Tricks
- GAMESS: Quick Run with MPI method
- Gaussian: Make Energy Convergence in Optimization Easy !
- Gaussian: Use B3LYP-VWN5 instead of B3LYP-VWN3
- Partial Recompile NWChem
- Post-HF: How to Select Active Space Orbital and Active Electron for Post-HF
- Q-Chem: How to run Q-Chem without “$QC/bin/qchem” script
Basic Compchem
- What is NVE, NVT, and NPT ?
- What do you guys do when you’re waiting for an experiment to finish ?
- Why all Quantum Chemistry programs use “Atomic Units” ?
- Why do Different Quantum Chemistry Programs give Different Results ?
Program Installations
- Installation of AMBER
- Installation of DALTON 2016 (& 2017)
- Installation of GAMESS
- Installation of GAMESS for OpenMP and MPI protocols
- Installation of GROMACS 2016 via yum
- Installation of GROMACS 4.x and FFTW3
- Installation of LAMMPS for RHEL and CentOS
- Installation of LAMMPS on Intel Xeon Cluster
- Installation of LAMMPS with GPU package
- Installation of Molden
- Installation of NWChem on RHEL & CentOS
- Installation of NWChem on RHEL & CentOS: Error and Solution
- Installation of ORCA
Test and Benchmarks
- Gaussian: Benchmark of G16 and Nvidia Tesla P100 GPU Acceleration
- Gaussian: Benchmark of G16 running on Intel Xeon Gold 6148
- LAMMPS: Benchmark of DPD Simulation on CentOS
- NWChem: Benchmark of DFT Calculation running on Ryzen Threadripper
- NWChem: Benchmark of Integral Evaluation Approaches
- NWChem: Benchmark of MPI Parallelization Efficiency for DFT calculation
- NWChem: Test for CCSD(T) & CCSD[T] calculation running on GeForce GTX 1050 Ti