[gmx-users] Deletion of Lipids During InflateGro?

Sanim Rahman sanimr at mail.usf.edu
Fri Dec 30 04:32:49 CET 2016

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?

I will deeply appreciate your assistance!

-Sanim Rahman

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