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
--
========================================
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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