[gmx-users] simulation at acid medium

[donna at iflysib.unlp.edu.ar]

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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