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
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
