[gmx-users] very strange area/lipid value for POPC membrane system
Peter C. Lai
pcl at uab.edu
Mon Aug 20 14:42:08 CEST 2012
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
> 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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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
(205) 690-0808 |
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