[gmx-users] chirality changes during the simulation

[Mark Abraham]

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