[gmx-users] simulation in acidic condition

[Justin Lemkul]

On 10/12/18 5:43 PM, ali khamoushi wrote:
> so, if I protonate my protein and then put it in neutral condition, is it
> going to work? I mean should I use particular ions for neutralization?

Plainly, there is no such thing as "pH" in an MD simulation. pH refers 
to the -log[H+], of which there are none in the MD simulation. So you're 
not putting anything into a "neutral condition." The protonation state 
is what you set it to be. If that reflects the dominant protonation 
state at some real-world pH value, then that's all it is. The rest of 
the solution doesn't have a pH.

Neutralization with ions is a separate issue. But neutralization of 
charge is not the same as "neutral pH."

-Justin

> On Sat, Oct 13, 2018 at 12:56 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> 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
>>
>> --
>> ==================================================
>>
>> 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
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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-- 
==================================================

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
http://www.thelemkullab.com

==================================================