How to select from a list of area_shrink_step.dat the correct one for my lipid bilayer system?

User discussions
1

GROMACS version: 20.02
GROMACS modification: Yes/No

Dear Gromacs users,

I have been using the inflategro.pl to compress a lipid bilayer with 100 popc lipids per layer around a centered ubiquinone molecule. After the script is done it generates a series of area_shrink#.dat per each step that contains the information about the average area per lipid.
How do I obtain the average area per lipid in A^2 from the numbers in this file? . I am assuming the numbers in this file are the coordinates for x, y, z in nm for the pbc box with the bilayer. The average area per lipid for POPC is around 69 A^2.
Appreciating any help on this in advance.
Thank you
Lazaro

2

The data file contains this information, but in nm2, so just divide the value by 100.

3

In the gromacs tutorial of KALP-15 in DPPC the shrink step 26 was choosen where shrink26.dat says 0.709 0.69 0.71. So I am assuming that you multiply any of this numbers by 100 because is in nm^2 as you mention?

4

Sorry, yes, multiply by 100.

5

Thank you for the clarification.
Cheers,
Lazaro