POPC membrane model in pH 4

From: zhjpan_at_mail.ustc.edu.cn
Date: Sat Sep 03 2011 - 09:36:58 CDT

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.
  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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