Adding Water and Starting Energy Minimization in LAMMPS | Session 5, Part 3

We pick up from the box containing five copies of the molecule prepared in the earlier parts. We load the water molecule template and start adding water to the box. Most of this session is spent getting the types and parameters to line up. Water needs its own atom, bond, and angle type numbers, along with the matching masses and coefficients. We run the input, read the errors, and fix them one by one. *Session files and earlier parts* GitHub repository: https://github.com/crisnapatel/nanosc... Session 5 folder: https://github.com/crisnapatel/nanosc... Part 1 video:    • Preparing PFAS and Water Models with Avoga...   Part 2 video:    • Packing FTOH Molecules and Loading OPLS Pa...   Full playlist:    • Molecular simulations   *Chapters* 00:00 Recap of the PFAS-water box 02:11 Periodic boundaries and molecules crossing the box 05:40 Unwrapping molecules in OVITO 07:19 Adding the water molecule template 09:12 Why the water atoms appear as carbon in OVITO 10:52 Reserving separate atom types for water 14:57 Offsetting the water type numbers 16:50 First water insertion run 18:18 Adding water bond and angle coefficients 20:05 Fixing the coefficient type numbers 21:43 Setting masses for the water atom types 23:32 Estimating how much water to add 26:10 Water models and equilibration 32:43 Calculating the target water count from box volume 34:34 Why the overlap check limits random insertion 35:57 A short discussion of MSD and diffusion 38:47 Pressure, temperature, and thermostats 42:47 Saving the combined system as a data file 43:42 Reading the data file in a new input 45:42 Choosing pair interactions 48:57 Extracting pair coefficients from the data file 53:37 Debugging the pair-coefficient input 55:47 Data-file coefficients versus pair_coeff I J 57:57 Geometric mixing for unlike atom types 1:01:22 Reformatting coefficients with awk 1:05:27 Trying the water insertion again 1:07:07 Preparing the energy-minimization input 1:10:22 Running the initial minimization 1:13:47 Writing a trajectory for OVITO 1:15:52 Inspecting the result and the remaining empty space #MolecularDynamics #LAMMPS #PFAS #WaterSimulation #OVITO #EnergyMinimization