From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Sep 03 2011 - 09:50:08 CDT
On Sep 3, 2011, at 10:38 AM, "zhjpan_at_mail.ustc.edu.cn"
> Hi,dear NAMDers
> I am a gromacs user but recently use a united-atom model to POPC(a phosphatidylcholine) membrane,then run a simultion at pH 4, which might protonate the protein embedded in the POPC.
> I roughly calculates what's pH 4 means:10^4 mol/dm^3=1/18000nm^3, about one H+ per 27nm cubic box.
Isn't pH 4 10^-4 mol/l?
> So H+ appear in a statistics case since there are much smaller space in water (in my case only 12*12*8).
> 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?
> If so, the protonation of protein will suppress.
> Do you have some advise for how to do?
> Zhijun Pan
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