[gmx-users] simulation at acid medium

Erik Marklund erik.marklund at chem.ox.ac.uk
Fri Jul 4 22:52:34 CEST 2014


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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