[gmx-users] Deletion of Lipids During InflateGro?

[Justin Lemkul]

On 12/29/16 10:32 PM, Sanim Rahman wrote:
> Dear Gromacs Users,
>
> I am working on building a lipid bilayer for my protein structure but I am
> having difficulty using the InflateGRO script.
>
> I am using a POPC bilayer and used the genconf command to extend the length
> of the bilayer so I would be able to go from having 128 to 256 lipids. The
> POPC bilayer I have is already converged so I plan to inflate the bilayer
> using InflateGRO, insert my protein in the center, and then converge to the
> appropriate lipid per area value with the script. My issue is that when I
> inflate the bilayer the script reduces the bilayer back to 128 lipids.
>
> I tried another approach by inflating my 128 lipid bilayer and then using
> the genconf command to obtain 256 lipids. However, when converging my
> bilayer, the lipids did not converge to the center of the entire system but
> the center of its own 128 lipid system, meaning that the bilayer split off
> into two separate pieces.
>
> Is there a way to have the script avoid reducing the number of lipids in
> the system in my original method?
>

Lipids will always be deleted by InflateGRO because some will overlap with the 
protein.  It won't delete 128 unless your protein really does occupy 50% of the 
membrane area.  Be sure you're using the right files as input.  If you need 
further help, please copy and paste your exact sequence of commands so we can 
see what you're doing.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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