[gmx-users] Different values of area per lipid with/without protein

Kulleperuma Kulleperuma kulleperuma.kulleperuma at mail.utoronto.ca
Thu Aug 23 19:39:10 CEST 2012

Hi all

I embedded the protein in POPC using inflategro. After the desired area per lipid (APL-0.64 A2) is reached I recalculated the APL with and without the protein.
I get two different values; with the protein - 0.64 and without the protein - 0.82.
I ran perl inflategro input.gro 1 POPC 0 output.gro 5 area.dat to get the above values.

I was expecting to get the same values for the two cases. Can someone explain the reason for this difference, since inflategro subtract the area of the protein in any case.

The size of the system is 6.5 6.5 7.5.

Thank you

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