[gmx-users] breaking lipid A tail in minimization

[Thomas Piggot]

By the way, the link to the paper needs to not include the final 
bracket: https://www.cell.com/structure/fulltext/S0969-2126(18)30132-1

On 14/06/18 18:40, Thomas Piggot wrote:
> 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.