[gmx-users] MD simulation at pH 2

Turgay Cakmak turgaycakmak34 at gmail.com
Fri May 9 15:45:18 CEST 2014

Hi all,

I have the 8-residue peptide and I want to do Molecular Dynamics
simulations at pH 2 (with explicit solvent).

To do this, I added three Hydrogen atoms to two of the 8-residue peptite
(one Hydrogen to the Glu, two Hydrojen to the Asp). And also I choose the
NH3 for the start terminus and COOH for the end terminus. Finally, I get
the my peptide at pH 2. And than, I plan to follow the usual procedure
(define box, fill the box with water, energy minim, md...)

But, still I am not sure whether this way is correct to get simulation at
pH 2 or not? Because when I look at the XXX.gro file (and also topol.top)
after the pdb2gmx –f XXX.pdb, I couldn’t see the new-added hydrogens.

If you could help me, I would be very happy.

with my best regards,


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