[gmx-users] KALP15 in DPPC

[negar habibzadeh]

I am doing  Simulation of *γ-AA*Peptide in DOPC Lipids  I am following
your tutorial  When I use inflategro script For my System I have got
Output System_inflated.gro file with certain message in Command prompt
as follows  . The Below Message Shows That There is No Lipid Molecules
Are Deleted  Should I Change the Cut-off or scaling Factor  to Delete
the Lipid Molecules or is it enough ,  I Mean  Must Some Lipid
Molecules Need to be Deleted ?

There are 128 lipids...
with 138 atoms per lipid..

Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet

Centering protein....
Checking for overlap....
...this might actually take a while....
100 % done...
There are 0 lipids within cut-off range...
0 will be removed from the upper leaflet...
0 will be removed from the lower leaflet...

Writing scaled bilayer & centered protein...


Calculating Area per lipid...
Protein X-min/max: 24    41
Protein Y-min/max: 23    43
X-range: 17 A    Y-range: 20 A
Building 17 X 20 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD....
lower TMD....
Area per protein: 3.25 nm^2
Area per lipid: 10.7582741393 nm^2

Area per protein, upper half: 2.25 nm^2
Area per lipid, upper leaflet : 10.7738991393 nm^2

Area per protein, lower half: 2.5 nm^2
Area per lipid, lower leaflet : 10.7699928893 nm^2

Writing Area per lipid...
Done!