[gmx-users] chirality changes during the simulation

[mu xiaojia]

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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