[gmx-users] simulation in acidic condition

Justin Lemkul jalemkul at vt.edu
Fri Oct 12 23:26:11 CEST 2018

On 10/12/18 5:14 PM, ali khamoushi wrote:
> hello everyone. I want to simulate a protein without ligand in gromacs in
> acidic conditions. but I don't know what exactly I must do. should I add
> HCL ions (for example) to turn neutral surrounding into acidic?
> my protein is Insulin. and I want to see behavior of his protein in acidic
> condition.

If you really want to monitor pH sensitivity, you should be doing a 
constant-pH simulation. For that, you need to look for other software, 
because you can't do those kinds of simulations in GROMACS.

Adding explicit HCl (which really should be H3O+ and Cl-) isn't 
appropriate either, because as soon as you have one hydronium ion in a 
simulation box, the pH is actually astronomically low (do the math and 
you'll see), and as well it's neither physically realistic nor useful.

The cheap approach that people often use is to simply protonate the 
biomolecule according to the dominant state at a given pH and simulate 
it that way. It's an approximation, but it may work.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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