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

Luís Carlos Filipe lcsfilipe at itqb.unl.pt
Fri Nov 1 13:53:45 CET 2013


Following up on Justin's reply I just want to add that, not only is it
possible, as it has been done before. For instance:

http://www.ncbi.nlm.nih.gov/pubmed/18214978
http://www.ncbi.nlm.nih.gov/pubmed/22072522

Luís Filipe
ITQB-UNL, Portugal

2013/11/1 Justin Lemkul <jalemkul at vt.edu>

>
>
> 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<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
>
>
>
>>
>>
>>
>> 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
>
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