[gmx-users] breaking lipid A tail in minimization

[Thomas Piggot]

What you are seeing sounds just like a periodic boundary visualisation 
issue 
(http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions). 
Also, the list doesn't accept attachments so we cannot see your 
modifications to the topology.

However, it's worth pointing out that a lipid A membrane will take ages 
to equilibrate in terms of membrane area (e.g see the "Extended All-Atom 
Simulations of E. coli Lipid A Membranes Using the CHARMM36 Forcefield" 
part of the methods section in some recent work I was involved in: 
https://www.cell.com/structure/fulltext/S0969-2126(18)30132-1). So to 
save you some considerable effort I will send you an equilibrated lipid 
A membrane off-list.

Cheers

Tom

On 14/06/18 09:49, Karim Mahnam wrote:
> Hello Dear GMX-users
> I want to do MD simulation on Lipid A membrane bilayer via gromacs software
> and G53A6 force filed.
> I get lamp_final.itp and one_lamp.gro from "Lipidbook Package  GROMOS-CKP
> Gromacs Lipid A" site.
> When I do steepest descent minimization with one Lipid A molecule in the
> water box, everything is Ok. But when I do steepest descent minimization
> with membrane contain 63 Lipid A (that I get from "
> http://www.charmm-gui.org/?doc=input/membrane" site and removed
> oligosaccharide heads) and 126 MG ions, it breaks lipid tail and hydrogen
> bonds with carbons.
>
> Would you please how can I solve this problem.
> How can I make a pre-equilibrated bilayer Lipid A  structure for G53A6
> forcefield?
> I attached topology file to this mail. (I changed only atom names in itp
> file according to Charmm27 force field, because  charmm-gui  make bilayer
> with Charmm27  atom name and as you know atom names are not important in
> itp file)
> Thank you very much
> Karim Mahnam, Associate professor of shahrkord university, Iran
>
>

-- 
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.