Simulating a protein or DNA with multiple ligands

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GROMACS version:2020.6
GROMACS modification: Yes/No
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I am a beginner with gromacs. I have just started to learn some basics. Can anybody help me regarding how to set up a system for performing a simulation of a protein/DNA molecule with multiple ligands. It can be different ligands altogether or simply multiple copies of one single ligand.

The approach that I am using is first I create the box around my protein or dna molecule and then add the ligands (say 5 or 10) using gmx insert molecules command. But I find that none of the time I have been able to perform the NVT and NPT equilibriation alongwith the final production MD run. The calculation is not at all running. It just stops after the energy minimisation step.

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Are you expecting the ligand to come and bind over time, or do you want to study how a ligand interacts within the binding pocket? If the latter is your aim, you should first dock the ligand and use the protein–ligand complex as the starting point for your simulation. You may want to begin with a protein–ligand tutorial. For multiple ligands, you can follow the same approach.

Also, we do not know what the error is. Simply saying that it is not running is not enough. It would be better to start with a tutorial and try multiple times.