I think you should start first with GROMACS tutorials - http://www.mdtutorials.com/gmx/

And also read GROMACS' documentation (:

Moreover, you could look for more specific guides, like this - https://sites.psu.edu/simtech/micelles/

Starting a molecular dynamics (MD) simulation involves several key steps:

1. Define Your System:

- Choose Your Molecules: Decide on the molecules or materials you want to simulate.

- Build Your System: Create a model of your system using software tools like VMD, PyMOL, or specialized molecular builders.

2. Prepare the Input Files:

- Topology File: Contains information about the types of atoms, bonds, angles, and other parameters.

- Coordinate File: Provides the initial positions of the atoms.

- Parameter File: Specifies simulation parameters such as temperature, pressure, and simulation time.

3. Select a Force Field:

- Choose a force field that defines how atoms interact. Common ones include AMBER, CHARMM, and GROMOS.

4. Set Up the Simulation Environment:

- Choose a Simulation Software: Examples include GROMACS, LAMMPS, and NAMD.

- Configure Parameters: Define settings such as time step, temperature control, pressure control, and the length of the simulation.

5. Minimize the Energy:

- Perform an energy minimization to relax the system and remove any bad contacts or unrealistic geometry.

6. Equilibrate the System:

- Run a short equilibration simulation to stabilize the system at the desired temperature and pressure.

7. Run the Production Simulation:

- Execute the full simulation to collect data over the desired time period.

8. Analyze the Results:

- Use tools to analyze the trajectory, calculate properties like diffusion coefficients, and interpret the data.

Each step requires specific software and techniques, so make sure to consult documentation and tutorials for the software you’re using.

Though I make use of material studio and my simulation is basically simulation of metals and inhibitors ( corrosion inhibiton)

Hello,

Better to use the basic tutorials given in the GROMACS website.

There are tons of tutorials in youtube which will give you clear cut idea about the use of of GROMACS

For basic file preparation you can use CHARMM-GUI (https://www.charmm-gui.org/?doc=input/solution) under Solution Builder in Input Generater section.

This is create all the files to rum simulations which can be further transferred to server or workstation to execute simulations.

Regards