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?
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