[gmx-users] Error in protein insertion in bilipid layer

Priya Das priyadas001 at gmail.com
Mon Dec 8 08:48:13 CET 2014

Dear All,

After insertion of my big proteinin lipid bilayer (512) moleules, i used
the command :

perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat

I get a area/ lipid : 10.231 nm2 and on shrinking i get 6. 89nm 2
after only 9 rounds of simulation.

But In the tutorial its around 26 rounds of iteration.

After this step when i solvate the system, there is a cavity at the
interface of hydrophobic region of protein and t

the membrane. There are a large number of unwanted water molecules
which i cannot delete manually.

Is there any mistake in inflate step; i mean nanometer and angstrom scale?

*Let us all join hands to save our " Mother Earth"*
Priya Das
Research Scholar
Dept. of Computational Biology and Bioinformatics,
University of Kerala

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