[gmx-users] analyzing docking + MD results

[MD]

Hi Gromacs folks,

I want to look at protein peptide interaction. After docking two
conformations of the peptide emerged, and both of which make chemistry
sense and have similar low binding energies. (+-1 kj/mol). The distance
between the two conformations of the peptide is ~8A.

Then I tried simulations on the two scenarios of protein peptide complexes
and the results showed the peptide only shifted very slightly in both
simulations. The rmsd, and energy dropping are all similar. I wonder if
there are other ways to make a judgement to tell which conformation of the
peptide makes more sense by analyzing their MD results?

Thanks,

Ming