Protein in Solution - mms-fcul/CpHMD-container GitHub Wiki

This tutorial will explain how to use the CpHMD container to perform simulations with stochastic-CpHMD on a simple protein in water. We will perform this tutorial with the GROMOS force field using only regular, already parameterized amino acids.

The system used for this tutorial will be hen egg lysozyme (HEWL) with the PDBid: 3lzt. Since no custom molecules will be required, the tutorial will outline all the steps necessary for a basic user to perform CpHMD simulations.

To get all tutorial files from the container into your directory use:

singularity run --app get-tutorials CpHMD.sif

The main topics of this tutorial are as follows:

  1. System building, minimization, and initialization
    1. Protein preparation
    2. System construction
    3. Index creation, Minimization and Initialization
  2. CpHMD settings editing
  3. CpHMD simulation
  4. CpHMD Analysis

Super advanced cheat sheet to run

  • First section
  1. Get and clean pdb
  2. pdb2cphmd | singularity run --app pdb2cphmd CpHMD.sif -p .pdb -f -r
  3. Gmx pdb2gmx | singularity exec CpHMD.sif gmx pdb2gmx -f ./_CpHMD.pdb -p .top -o .gro -ignh -renum -ter
  4. Gmx editconf (build box)
  5. Gmx solvate (solvate box)
  6. Gmx Make_ndx | singularity exec CpHMD.sif gmx make_ndx -f _solv.gro -o index.ndx
  7. Minim + init
  • Second section
  1. Cphmd settings preparation
  2. Make sites test
  3. run CpHMD | singularity exec --nv --bind $HOME CpHMD.sif /CpHMD/scripts/CpHMD.sh CpHMD-basic.settings
  4. Analysis

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