Dear GMX users, 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?
Thanks very much for any suggestion! Jia
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