Dear GMX users,<div><br></div><div>I have some trajectories of Ala-Ala dipepetides with COOH terminals (Cap-Ala-Ala-COOH), However, I saw the chirality of the Ala-COOH doesn't maintained as L form during the simulation, there are D-forms, is it because there are some lacks of parameters of this part or Gromacs doesn't have specific parameters to prevent chirality flipping?</div>
<div><br></div><div>Thanks very much for any suggestion!</div><div><br></div><div>Jia</div>