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

zhjpan at mail.ustc.edu.cn zhjpan at mail.ustc.edu.cn
Sat Sep 3 17:07:11 CEST 2011

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?

Zhijun Pan
E-mail:zhjpan at mail.ustc.edu.cn
MSN:d2denis at msn.cn

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