Re: Re: POPC membrane model in pH 4

From: zhjpan_at_mail.ustc.edu.cn
Date: Sat Sep 03 2011 - 10:12:06 CDT

yes,of course,"L" is one liter ,means dm^3=10^-3 m^3. Next is to convert mol into 6.02 *10^23 number of molecule.

> -----Original E-mail-----
> From: "Axel Kohlmeyer" <akohlmey_at_gmail.com>
> Sent Time: 2011-9-3 22:50:08
> To: "zhjpan_at_mail.ustc.edu.cn" <zhjpan_at_mail.ustc.edu.cn>
> Cc: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
> Subject: Re: namd-l: POPC membrane model in pH 4
>
> On Sep 3, 2011, at 10:38 AM, "zhjpan_at_mail.ustc.edu.cn"
> <zhjpan_at_mail.ustc.edu.cn> wrote:
>
> > 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
> > Tel-HeFei:(86)-13655519036
> > E-mail:zhjpan_at_mail.ustc.edu.cn
> > MSN:d2denis_at_msn.cn
> >
>

```--
Zhijun Pan
Tel-HeFei:(86)-13655519036
E-mail:zhjpan_at_mail.ustc.edu.cn
MSN:d2denis_at_msn.cn
```

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:46 CST