Protein in Solution: Index Creation, Minimization, and Initialization - mms-fcul/CpHMD-container GitHub Wiki
In this step we will deal with creating the correct index for the future CpHMD simulation and perform both a system minimization and initialization.
Important
This is a crucial step for the success of CpHMD simulations! When running CpHMD in the future, the framework will perform continuum electrostatic calculations on our system, having the solutes explicit and treating the water as an implicit medium.
For this reason the index needs to have a group with all the solutes in our system box called [ Protein ].
Like before, if the user wants, the container GROMACS can be used to create the index. Since we are dealing with a simple protein, the automatic index creation tool already gathers all the protein into the [ Protein ] group.
If other molecules are present in the system in interaction with the protein (solvent excluded), these should also be included in the [ Protein ] group for CpHMD recognition and correct assignment in the continuum electrostatics treatment (Poisson-Boltzmann/Monte Carlo cycle)
In this tutorial
singularity exec CpHMD.sif gmx make_ndx -f HEWL_solv.gro -o index.ndx
The specific groups present in your system can be tailored by the user, with the exception of the previously described [ Protein ].
These two steps were combined since they will not be explored in depth for this tutorial.
Details on the setup of minimization and initialization of a protein system can be found in regular MD tutorials.
The .mdp files for minimization and initialization will be provided in the Protein in Solution tutorial folder, but no details on how to build them will be given here.
In the tutorial, both the minimization (01_min.sh script) and initialization (02_init.sh script) were run with GROMACS within the container.
