[gmx-users] Lysozyme in Water at different pH and Ionic strength

[Justin Lemkul]

On 11/1/13 8:39 AM, xiao wrote:
> It is impossible. But you can add proton to the acidic amino acid.
>

It's certainly not impossible.  There are constant-pH methods that exist; the 
list archive contains many posts on this topic, and more information can be 
found at:

http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation

Whether or not you can easily accomplish such simulations in Gromacs is another 
matter.

Standard MD does not allow for dynamic protonation states, so the closest you 
can get without running more advanced MD is to use fixed protonation states, 
assigned by pdb2gmx, that are indicative of the most prevalent state of the 
residues at a given pH value.

Changing ionic strength is trivial; that's what genion -conc is for.

-Justin

>
>
>
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> At 2013-11-01 20:36:41,Mass <masstransfer_2010 at yahoo.com> wrote:
>> Dear Gromacs users,
>> Just was wondering if it is possible to protein solution let say Lysozyme in Water example of Justin tutorial at different pH and ionic strengths, if so how?
>> Thanks
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-- 
==================================================

Justin A. Lemkul, Ph.D.
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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