[gmx-users] Ion flux through membrane protein

[Maximilien LOPES RODRIGUES]

 Hello Carsten, thank you very much for your answer.

I read the GROMACS manual and your papers. The new method you developed seems very interesting and accurate but it appears much more complicated than expected. I don't know if I will be able to properly run a such simulation. I still have so much to learn

Basically, these are the main questions I want to answer by simulation:
- Is my protein more permeable to anion or cation ?
- Is it more selective for K+ or Na+ (for instance) ?
- Does this solute pass through the channel and how ?

I am not sure if calculating an exact flux is very relevant now. I should have wrote a more accurate title for my first question, sorry !

There are numerous papers about ions transport through membrane protein but they don't explain how to reproduce (step by step) such simulation.

Thank you again.
Kind regards,
Max
 
 
Le Jeudi 26 Mai 2016 11:58 CEST, gromacs.org_gmx-users-request at maillist.sys.kth.se a écrit: 

> Hi Maximilien,
> 
> depending on what exactly the questions are that you like to address, the double-membrane
> setup as used in computational electrophysiology setups might be helpful for you.
> There is a section in the GROMACS PDF manual about that, and there are these two papers:
> http://www.sciencedirect.com/science/article/pii/S0005273616300360
> http://www.mpibpc.mpg.de/275657/Kutzner_2011_BPJ_101_809-817.pdf
> 
> Best,
>  Carsten
> 
> > On 26 May 2016, at 10:19, Maximilien LOPES RODRIGUES <maximilien.lopesrodrigues at unamur.be> wrote:
> > 
> > Dear GROMACS users,
> > 
> > first of all, thank you for paying attention to my question.
> > 
> > I have a system containing a membrane protein (porin) that is embedded in a lipid bilayer (XY).
> > I would like to investigate the flux of ions (or other solutes like sugar) that can pass through the protein.
> > Unfortunately, I don't know the general rules to make a such simulation.
> > 
> > - Can I just add a higher concentration of ions in one side ? (if yes, should I suppress PBC in Z axis ?)
> > - Do I put the counter ions on the same side ?
> > - So, do I have to make PBC condition only on XY plan ?
> > - Is there an external electrical field to apply ? If yes, how ?
> > 
> > If you have general tutorial documentation, I would be happy to take a look at it !
> > 
> > Thank you !
> > Kind regards,
> > Maximilien Lopes Rodrigues
> > 
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