I guess you can do different kind of biophysical inquiry like H-Bond formation between the residues involved in interaction. Pair-wise distance calculation between residues which are supposed to interact between protein-peptide. If you are expecting any specific kind of interaction like cation-pi, pi-pi, aromatic-aromatic and so on, then focus your inquiry in that line.

To know about the strength of interaction you might have to do statistical calculation of different conformational states (Here it is interaction state). First make sure that your simulation have reached asymptote.

Dear friend,

Most important analysis in your field is :

1- H-bond calculation to determine hydrogen bonds in your system

2- alanine scanning

3- binding free energy calculations (TI , MMPBSA , LIE ,... methods)

....

Hope it helps,

HHA

Thank you for your answers. How can I check that my simulation have reached asymptote? Which residues alanine scanning I should check, only protein binding site? I try to calculate LIE method, should I use other methods to determine the binding strenght?

The simulation period depends on many factors but simply using equilibration phase can ensure you that your system is equalized. For more in formation read simulations manuals and tutorials (I suggest AMBER for simulation).

In alanine scanning, You can choose residues from binding site also yo can choose them from online server results such as :

http://ef-site.hgc.jp/eF-site/index.jsp

The third method is using graphical software (e.g chimera) to count residues with a fixed distance from your ligand.

As an answer to your second question I should notice that LIE is a weak method and I prefer TI and mmpbsa methods.

Best,

HHA