Very interesting series on the top 10 algorithms with the greatest influence on the development and practice of science and engineering in the 20th century. Metropolis Algorithm for Monte Carlo...

Overview Part 1 established that above the critical entanglement molecular weight $M_c$, polymer chains form a persistent topological network. This post asks the next question: what are the mechan...

Chain Entanglement: A Purely Topological Effect Polymer chains have no covalent bonds between them — yet long chains resist flow in a way short ones do not. The reason is purely topological: chain...

The standard error of the mean of $N$ independent measurements is: [\boxed{\mathrm{SE} = \frac{\sigma}{\sqrt{N}}}] Most derivations establish this in two lines of algebra and move on. The $\sqrt{...

Tools fftool This is a Python tool to build force field input files for molecular dynamics simulations of systems composed of molecules, ions or extended materials. IOData IOData is a free and op...

Gromacs trr file Files with the trr file extension contain the trajectory of a simulation. In this file all the coordinates, velocities, forces and energies are printed as you told GROMACS in your...

Basis Compare two folders, 比較兩個目錄內檔案的差異，列出所有差異處 diff -bur folder1/ folder2/ 比較兩個目錄內檔案的差異，只列出有差異的檔案名稱 diff -qr folder1/ folder2/ diff -qr folder1/ folder2/ | sort Handle files with patterns Rem...

Convert g96 to xyz gmx editconf -f input.g96 -o output.gro obabel input.gro -O output.xyz

SPACK Showing installed version of a package spack find [option] <package name> $ spack find -v gromacs load package spack load <package name> Compiler spack find -p gcc -- linux-ub...

Basis sets and pseudopotentials Which basis sets and/or pseudopotentials should I use? When in doubt, always use the DZVP-MOLOPT-GTH basis set and the GTH-PBE pseudopotential. use OT for non-m...