[gmx-users] About APL And Shrunken System Size

[vidhya sankar]

I gave My cmd Prompt output for  satisfactorily shrunken 
system  as follows  


Reading..... 
Scaling lipids....
There are 127 lipids...
with 50 atoms per lipid..
Determining upper and lower leaflet...
64 lipids in the upper...
63 lipids in the lower leaflet 
Centering protein....
Writing scaled bilayer & centered protein...
Calculating Area per lipid...
Protein X-min/max: 98    119
Protein Y-min/max: 99    117
X-range: 21 A    Y-range: 18 A
Building 21 X 18 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD....
lower TMD....
Area per protein: 3.75 nm^2
Area per lipid: 6.60886502362205 nm^2
Area per protein, upper half: 2.75 nm^2
Area per lipid, upper leaflet : 6.572858265625 nm^2
Area per protein, lower half: 3 nm^2
Area per lipid, lower leaflet : 6.67322109523809 nm^2
Writing Area per lipid...


In  the final Energy minimization  (.gro file) of the satisfactorily shrunken 
system  The Box vectors  Has been Increased form 6 6  6 6 to
 20.57700  20.57700   6.00000

Then  As you Told Me the There  is Something wrong Because   Such Large x-y Area is not Possible with Quoted  APL ( 6.60886502362205 nm^2)
May I Increase the Initial box size ? 

Why this Happens and  Where I have Committed the Mistake ?  My system is Cyclic Peptide I am grateful if you Give suggestion and Commments

Thanks In Advance










Done!