[gmx-users] very strange area/lipid value for POPC membrane system

[Peter C. Lai]

Also important to ask is:
What was your APL *before* you inserted the protein? Was it realistic to 
begin with? If not, then start your problem solving there...

On 2012-08-19 06:16:48PM +0200, Albert wrote:
> Dear All:
> 
>   I am using GridMAT-MD to calculate the area/lipid for my POPC system. 
> The whole system was consist of a 300aa protein, 116 POPC and 0.15M NaCl.
> 
> 
> 1. I calculate the area/lipids by GridMAT-MD with the protein in it and 
> I got a value:
> 
> Ave APL = 54.1013569676733 sq. Ang
> 
> 2. I removed the protein and I get another value:
> 
> Ave APL = 76.1121752016697 sq. Ang
> 
> Do you have any idea what happen for my calculation?  Of course I truned 
> the line "protein    yes/no" for case with/without protein in the 
> example param file. What need to mention is that both values are far 
> from the POPC real area/lipids which should be something around 64.
> 
> Does anybody knows what happen?
> 
> thank you very much
> 
> best
> Albert
> 
> 
> here is paramters:
> 
> 
> ###### Input file and input file parameters
> 
> bilayer            eq-withProtein.gro
> solvent            SOL
> ions            NA+,CL-
> 
> resname          POPC
> atomname        P1,C1
> 
> ###### Define the size and shape of the grid
> 
> box_size        vectors
> vectors            6.57174,6.89896,9.23361
> grid            20
> conserve_ratio        yes
> 
> ###### Define whether there is a protein embedded in the bilayer
> 
> protein            yes
> precision        1.3
> P_value            5.0
> 
> ###### Define the desired output files
> 
> top_pbc            no
> bottom_pbc        no
> average_pbc        no
> 
> top_area        yes
> bottom_area        yes
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-- 
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Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
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