Octane in a water box under CHARMM36 forcefield.
The following steps are to be completed:
- Create a water box
- Insert octane molecules into the box
- Do energy minimization, NVT and NPT equilibration
- Run the full simulation for ~10ns
The files required for this:
- GROMACS, which can be downloaded from here: http://manual.gromacs.org/documentation/2020.1/download.html
- CHARMM36.ff forcefield folder, which can be found here: http://www.gromacs.org/@api/deki/files/184/=charmm36.ff_4.5.7_ref.tgz
- PDB file of octane: https://ww2.chemistry.gatech.edu/~lw26/structure/small_molecules/octane.pdb (it has to be changed to match the forcefield)
- minim.mdp file, nvt.mdp and npt.mdp files: these are all uploaded in the mdp file section
It is also recommended to do this on a supercomputer, or just run shorter mdrun.