[gmx-users] About APL And Shrunken System Size
jalemkul at vt.edu
Thu Nov 1 17:52:41 CET 2012
On 11/1/12 12:48 PM, vidhya sankar wrote:
> I gave My cmd Prompt output for satisfactorily shrunken
> system as follows
What was your command that produced this output?
> 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
Please use real file names and tell me where this comes from.
> 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)
Yes, it is absolutely impossible to have that APL in a system that has an x-y
area of over 42000 A^2. I suspect you're confusing your files.
> May I Increase the Initial box size ?
I have already suggested that you make no manual modifications to box vectors.
> Why this Happens and Where I have Committed the Mistake ? My system is Cyclic Peptide I am grateful if you Give suggestion and Commments
Please answer all questions posed above directly. I suspect you are mixing up
files but I can't possibly guess what is going on. Your assertions do not add
up and I can't suggest a resolution without complete information.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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