[gmx-users] simulation at acid medium

[donna at iflysib.unlp.edu.ar]

Hi Erik

Thanks for your hints
Sorry,  I have problems with internet, so I could not answer you before


I thought something was wrong with the MD simulation at physiological solution
since it looks like as a  MD simulation at water. But I did not take into
account the protonation states!!!

Please, do you Know any another form to have acid medium?.
    thanks again,
        Chris

Erik Marklund <erik.marklund at chem.ox.ac.uk> ha escrito:

> Then you essentially need to protonate the side chains according to   
> their pKa and the pH. Note that the protons will not hop around   
> between groups in normal MD. What makes you think something's wrong   
> with your physiological solution?
>
> Kind regards,
> Erik
>
>
> On 4 Jul 2014, at 19:47, donna at iflysib.unlp.edu.ar wrote:
>
>> Hi Erik
>>
>> Thanks.
>> Details:
>> System: proteins
>> Properties: those ones for which there are analyzes tools in Gromacs
>>
>> I am trying to model some proteins at acid medium.
>> I use MD with water and I create a physiological solution from the   
>> counterion tool of Gromacs,  But I think something is wrong.
>>
>> To analize properties: I use RMSD of alfa carbons to test the   
>> converge of the MD.  Also the idea is to analyze the giration radii  
>>   and the fluctuations through the Raddi of Giration and the RMSDF   
>> tools that gives Gromacs.
>>
>> I realize now that Ia use the neutral protonate states for the   
>> proteins when I use the physiological solution, and this is an   
>> error. So, the results in RMSD, RG and RMSDF should be different   
>> from those that I have now.
>> Sorry, I'm not a chemistry nor a biochemistry. I am a physics, so I  
>>  have some missing concepts.
>>
>>  Kind regards
>>          Chris
>>
>> I do not known if it is another different way to do the medium
>>
>> Erik Marklund <erik.marklund at chem.ox.ac.uk> ha escrito:
>>
>>> Hi Chris,
>>>
>>> This very much depends on what system you are studying and what    
>>> properties you aim to look at. Could you provide more detail please.
>>>
>>> Kind regards,
>>> Erik
>>>
>>> Erik Marklund, PhD
>>> Postdoctoral Research Associate
>>>
>>> Department of Chemistry
>>> Physical & Theoretical Chemistry Laboratory
>>> University of Oxford
>>> South Parks Road
>>> Oxford
>>> OX1 3QZ
>>>
>>> On 4 Jul 2014, at 16:45, donna at iflysib.unlp.edu.ar wrote:
>>>
>>>> Dear all
>>>> Please, I need help.
>>>> I have to do a simulation at an acid medium (PH = around 5 or 6).
>>>> Is it sufficient to work with normal water,from it
>>>> to create a physiological solution (Ph=around 5) and then
>>>> to work with the physiological solution?
>>>> I would very much appreciate any clues in this regards
>>>>
>>>>   Chris
>>>>
>>>> Dra. M. Cristina Donnamaria
>>>> Instituto de Fisica de Liqidos y Sistemas Biologicos
>>>> -IFLYSIB-
>>>> Comision de Invegtigaciones Cientificas de la Prov.
>>>> de Bs. As. Argentina
>>>>
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