I run MD simulations using GROMACS of a protein in the apo and holo form and I have to analyse the differences between the two forms. What kind of tests that can be performed?
Interesting question, I came across the attached paper while searching on this topic, and I think one way to benefit from MD is to observe the conformational changes in the ligands and the catalytic site e.g. ligand dihedral angles.
Good luck!
Article Differences Between Apo and Three Holo Forms of the Intestin...
The simplest analysis that you can perform are RMSF, RMSD, Hydrogen bonding (with itself and solute), secondary structure analysis. You can also analyze if the protein known to have conformational transition based on simple distance between residues. The radius of gyration will give you an idea about its compactness. RDF of solute around the protein will give you an idea of solvent distribution and so on...
The analysis of MDsimulation data depends on what you are actually looking for. You need to decide that first even before running a simulation.
In additional, I would recommend to perform covariance matrix calculations in apo and holo forms from MD simulation snapshots. This could help you to analyze the internal motion position fluctuations correlations between different residues and study the differences in apo and holo forms. You may also try to analyze salt-bridges along each trajectory (in apo and holo forms).
This is quite problem dependent. For instance, you could check the differences of mobility (via RMSD calculations) of the ligand and the residues lining the ligand-binding pocket in, respectively, apo and holo forms.