# How to select from a list of area\_shrink\_step.dat the correct one for my lipid bilayer system?

**URL:** <https://gromacs.bioexcel.eu/t/how-to-select-from-a-list-of-area-shrink-step-dat-the-correct-one-for-my-lipid-bilayer-system/3775>\
**Category:** User discussions\
**Created:** [March 3, 2022, 3:14pm UTC](https://gromacs.bioexcel.eu/t/how-to-select-from-a-list-of-area-shrink-step-dat-the-correct-one-for-my-lipid-bilayer-system/3775 "2022-03-03T15:14:24Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Lazaro](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/lazaro/32/93_2.png) [@Lazaro](https://gromacs.bioexcel.eu/u/Lazaro)\
**Post date:** [March 3, 2022, 3:14pm UTC](https://gromacs.bioexcel.eu/t/how-to-select-from-a-list-of-area-shrink-step-dat-the-correct-one-for-my-lipid-bilayer-system/3775/1 "2022-03-03T15:14:24Z")

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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

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [March 3, 2022, 3:32pm UTC](https://gromacs.bioexcel.eu/t/how-to-select-from-a-list-of-area-shrink-step-dat-the-correct-one-for-my-lipid-bilayer-system/3775/2 "2022-03-03T15:32:02Z")

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> [@Lazaro](#):
>
> How do I obtain the average area per lipid in A^2 from the numbers in this file?

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

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**Author:** ![Lazaro](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/lazaro/32/93_2.png) [@Lazaro](https://gromacs.bioexcel.eu/u/Lazaro)\
**Post date:** [March 3, 2022, 3:45pm UTC](https://gromacs.bioexcel.eu/t/how-to-select-from-a-list-of-area-shrink-step-dat-the-correct-one-for-my-lipid-bilayer-system/3775/3 "2022-03-03T15:45:30Z")

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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?

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [March 3, 2022, 3:56pm UTC](https://gromacs.bioexcel.eu/t/how-to-select-from-a-list-of-area-shrink-step-dat-the-correct-one-for-my-lipid-bilayer-system/3775/4 "2022-03-03T15:56:40Z")

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Sorry, yes, multiply by 100.

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**Author:** ![Lazaro](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/lazaro/32/93_2.png) [@Lazaro](https://gromacs.bioexcel.eu/u/Lazaro)\
**Post date:** [March 3, 2022, 3:57pm UTC](https://gromacs.bioexcel.eu/t/how-to-select-from-a-list-of-area-shrink-step-dat-the-correct-one-for-my-lipid-bilayer-system/3775/5 "2022-03-03T15:57:06Z")

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Thank you for the clarification.  
Cheers,  
Lazaro