[gmx-users] About APL And Shrunken System Size

[Justin Lemkul]

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?

>
> 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
>

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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