On 6/06/2012 8:31 AM, mu xiaojia wrote:
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?
This depends on your force field and simulation protocol, not on the
software with which you implement it.
Mark
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