[gmx-users] MD simulation at pH 2

Justin Lemkul jalemkul at vt.edu
Fri May 9 15:57:59 CEST 2014

On 5/9/14, 9:45 AM, Turgay Cakmak 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.

No, that's not a simulation at pH 2, but it is a simulation of the predominant 
form of the peptide at pH 2.

The missing piece of the puzzle here is what your actual pdb2gmx command was. 
If you didn't tell pdb2gmx to protonate Glu and Asp (using -glu and -asp, 
respectively), then it will default to the "normal" deprotonated forms.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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