[gmx-developers] will united-atom POPC forcefield mater in pH 4

[chris.neale at utoronto.ca]

Zhijun:

This is a question for the gmx-users list, so I will address it there.  
Please keep this type of question on the users list.

> 1.Are hydrogen ion H+ probably bind to POPC's phosphate O atom when  
> I randomly assign it?

That sounds a lot like something that you can test. Na+ ions do not  
form long-lived interactions like this during simulation (spending  
much more time in bulk water than in particular interactions with  
individual lipids), so I doubt it.

> 2.Will hydrogen ion (so small) channel the POPC lipid, while a  
> full-atom is not?

Your question is not well formed. Do you mean "will the hydrogen ion  
pass between the lipids, across the bilayer in united-atom but not  
all-atom simulations"?

Again, that sounds like something that you can test. It would  
eventually cross both types of bilayers (in the limit of infinite  
simulations) but no, I doubt that you would observe this in obtainable  
simulation timescales.

Chris.

-- original message --

Hi,dear NAMDers
   I am a gromacs user but recently run a simultion at pH 4, which  
might protonate the protein embedded in POPC(a phosphatidylcholine)  
membrane.But I'm using a united-atom model to POPC develop by Erik  
Lindahl and Peter Kasson(2010), base on Berger lipids ported to  
Gromacs/AMBER forcefields(1997).
    I roughly calculates what's pH 4 means:10^4 mol/dm^3=1/18000nm^3,  
about one H+ per 27nm cubic box.
   There are two things I am not quiet sure :
   1.Are hydrogen ion H+ probably bind to POPC's phosphate O atom when  
I randomly assign it?
   2.Will hydrogen ion (so small) channel the POPC lipid, while a  
full-atom is not?
   Do you have some advise for how to do? Or a full-atom model for POPC better?