[gmx-users] min + capped peptide

[Bahar Mehrpuyan]

Hi gmx users

I want to cap my peptide (adding ACE & NAC) with Avogadro package , my question is , should I minimize the capped peptide with forcefields(molecular mechanics) available in avogadro, then use it in the simulation? or just simulation procedures (minimization and equilibration) is sufficient for minimizing the peptide structure.

thanks in advance