Protein Membrane CpHMD system tutorial. - mms-fcul/CpHMD-container GitHub Wiki

In this tutorial, we will learn the steps to prepare a CpHMD simulation using a peptide in a membrane system. The steps described in this tutorial can be expanded to protein systems.

We will be using the CHARMM36m force field in our simulations of a glu pentapeptide system, with its termini capped, in a system box containing a POPC(80)/POPG(20) mixture membrane.

This tutorial assumes you are in possession of the following files:

• Protein structure (.pdb)
• Hydrated membrane structure and topology (.pdb and .top)
• Membrane lipid .itps

In this tutorial, we assume the membrane lipids are not included in the force field but as external .itp, therefore, they will be treated as includes in the topology file.

• System building, minimization, and initialization
  1. Getting CpHMD container
  2. Peptide Preparation
  3. Membrane Preparation

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