[gmx-users] About APL And Shrunken System Size
scvsankar_agr at yahoo.com
Thu Nov 1 17:48:46 CET 2012
I gave My cmd Prompt output for satisfactorily shrunken
system as follows
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
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..
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
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