Analyzing source code of Colvars package In this post we look at some parts of the source code of the Colvars package (module). Compilation with COLVARS_DEBUG To get a understanding …
Use AMBER forcefields in NAMD Online resources The official website of AMBER forcefield contains lots of useful information. Relevant parameters in NAMD to enable AMBER …
Prepare MD simulations in NAMD We show how to prepare MD simulations for alanine dipeptide and chignolin with NAMD. To do this, one typically builds a PSF file first …
Build Gromacs with Colvars and PLUMED support Required packages 1.1. Colvars I used a modified version of Colvars, which requires LibTorch package. In general, it suffices to work with …
MD packages This post lists several software packages and tools that are useful in molecular simulations. MD simulation packages OpenMM: a …