[gmx-users] Difference between POPI and DOPI membranes? and about lipid headgroups

[Mijiddorj Batsaikhan]

Dear James,

Thank you very much for your helpful suggestion.

Best regards,



Message: 3
Date: Wed, 19 Oct 2016 22:57:15 +0100
From: jkrieger at mrc-lmb.cam.ac.uk
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Difference between POPI and DOPI membranes?
        and about lipid headgroups
Message-ID:
        <cfdd105d169d798b20da73dc53537f84.squirrel at mail.mrc-lmb.cam.ac.uk>
Content-Type: text/plain

My suggestion is to mix and match parameters to extend from overlapping
regions. I did that to model GABA from glutamate and lysine. I just found
this thread via a google search that suggests DOPC and POPI
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2014-2015/2406.html

Best wishes
James

> Dear gmx users,
>
> I would like to simulate DOPI membrane system. I could not find DOPI
> membrane model from Charmm-gui, and I read that the closest one is POPI
> bilayer. I checked atoms of the lipids. First, there are carbons end of
> one
> tail needed to DOPI. Second, I need to change bond type from double to
> single in the middle of two tails.* (1) *Can I use the parameters of the
> POPI for DOPI membrane?
>
> In the head groups (PO4), there is a protonated oxygen in DOPI membrane
> figure. *(2).* Can I use deprotonated head group for my simulations?
>
> Please, suggest and advice me?
>
>
> Best regards,
>
> Mijiddorj
> --