[gmx-users] MD simulation at pH 2

[Dr. Vitaly Chaban]

Nice to know that acidic pH simulations are that easy.

Why do you conclude that you achieved pH 2?

Dr. Vitaly V. Chaban


On Fri, May 9, 2014 at 3:45 PM, Turgay Cakmak <turgaycakmak34 at gmail.com> wrote:
> 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,
>
> Turgay
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