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

[jkrieger at mrc-lmb.cam.ac.uk]

I notice that both papers mention modifications to GROMACS and cite the
following:
http://www.ncbi.nlm.nih.gov/pubmed/16471903

> 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
>>
>> 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 <jalemkul at outerbanks.umaryland.edu>
>> | (410)
>> 706-7441
>>
>> ==============================**====================
>>
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