[gmx-users] Coarse grain membrane simulation of DPPC

[Tsjerk Wassenaar]

Hi Ali,

Coarse grain and atomistic system probably respond differently to high
pressures.

Cheers,

Tsjerk
On Feb 29, 2016 21:23, <khourshaeishargh at mech.sharif.ir> wrote:

>
>
>
>
>         Dear all
>
>
>         Recently I saw  an article about 128DPPC  of lipid bilayer. it
> says that the bilayer would rupture by a
> lateral 200bar tension, using Gromacs all atom. now I want to gain that
> using coarsegrain method. for all atom the pdb file is obtainable but for
> CG, I built it using :
>
>
>         python insane.py -l DPPC -x 6 -y 6 -z 7.498 -pbc cubic -sol w -o
> dppc.gro
> -p system.top
>
>
>         I do minimization and NPT equilibrium. but when I load it with
> 200bar or
> even 100 bar the system fail less than 1ns but the article gain for 200
> bar, a time period of 8ns  and for 100 bar, no pore formation. oddly
> when I load it with 50bar I can elicit the correct answer for Area per
> lipid for the example.( I obtain 0.74 which is ok based on the
> article)
>
>
>         any comment on where probably I was wrong ? I really apreciate it.
>
>
>         best regards
>
>
>         Ali
>
>
>         ==================
>
>
>         Ali khourshaei shargh (khourshaeishargh at mech.sharif.ir)
>
>
>         Department of Mechanical Engineering
>
>
>         Sharif University of Technology, Tehran, Iran
>
>
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