[gmx-users] very strange area/lipid value for POPC membrane system

[Albert]

Dear All:

  I am using GridMAT-MD to calculate the area/lipid for my POPC system. 
The whole system was consist of a 300aa protein, 116 POPC and 0.15M NaCl.


1. I calculate the area/lipids by GridMAT-MD with the protein in it and 
I got a value:

Ave APL = 54.1013569676733 sq. Ang

2. I removed the protein and I get another value:

Ave APL = 76.1121752016697 sq. Ang

Do you have any idea what happen for my calculation?  Of course I truned 
the line "protein    yes/no" for case with/without protein in the 
example param file. What need to mention is that both values are far 
from the POPC real area/lipids which should be something around 64.

Does anybody knows what happen?

thank you very much

best
Albert


here is paramters:


###### Input file and input file parameters

bilayer            eq-withProtein.gro
solvent            SOL
ions            NA+,CL-

resname          POPC
atomname        P1,C1

###### Define the size and shape of the grid

box_size        vectors
vectors            6.57174,6.89896,9.23361
grid            20
conserve_ratio        yes

###### Define whether there is a protein embedded in the bilayer

protein            yes
precision        1.3
P_value            5.0

###### Define the desired output files

top_pbc            no
bottom_pbc        no
average_pbc        no

top_area        yes
bottom_area        yes