Memory Requirements for Parallel Calculations %Mem=128MW Memory required by each multiprocessor. %NProcShared=2 Use two shared memory processors on e...
Story: no one knows what entropy really is
In the case of Shannon’s measure the naming was not accidental. In 1961 one of us (Tribus) asked Shannon what he had thought about when he had finally confirmed his famous measure. Shannon replied:...
Lars Onsager (1903–1976)
兩位飄浮在耶魯校園的寂寞天才(下) 陽春白雪又何妨 by 高崇文
Transport equations
### Onsager’s regression hypothesis states that fluctuations evolve according to the laws that govern macroscopic variations. Boltzmann equation the derivation of Euler, Navier–Stokes, Burnett, a...
ORCA
ORCA ORCA is an ab initio, DFT, and semi-empirical SCF-MO package developed by Frank Neese et al. at the Max Planck Institut für Kohlenforschung. Orbital and density plots If you run a calculation...
Ab initio molecular dynamics (AIMD)
AIMD ORCA Molecular Dynamics Module Here is a nice example given by Dr. Martin Brehm. Also the metadynamics on top of AIMD.
References of quantum computing
BCG: The Race to Quantum Advantage Depends on Benchmarking McKinsey: Quantum computing use cases are getting real—what you need to know
GROMACS
Gromacs File formats tpr file tpr file extension stands for portable binary run input file. This file contains the starting structure of your simulation, the molecular topology and all the simula...
Debye-Hückel Theory
Electrolyte Debye-Hückel Theory (only valid for dilute solutions) In electrolyte, the ions are surrounded by clouds of charge opposite their own, due to the attractive forces of the opposing char...
MDAnalysis
MDAnalysis Atoms, residules, and segments The data structure in MDAnalysis Source: https://userguide.mdanalysis.org/stable/groups_of_atoms.html Selecting atoms Numerical ranges can be written ...