On 22/08/2012 3:47 PM, Albert wrote:
On 08/22/2012 07:44 AM, Mark Abraham wrote:
I don't see how this relates to your claim that you computed a value
with GridMAT that doesn't relate to a value computed some other way.
Mark
HI Mark:
thanks for kind reply.
here is my parameter for for calculation. The vector values was take
from the bottom of .gro file.
###### Input file and input file parameters
bilayer npt.gro
solvent SOL
ions NA+,CL-
resname POPC
atomname P1,C1
###### Define the size and shape of the grid
box_size solvent
vectors 6.84452,6.84452,9.80113
grid 20
The authors use a 200x200 grid in their first published work with this
tool. What makes you think 20 is enough? (And even if it is enough, you
still haven't demonstrated another calculation showing that the APL with
the embedded protein should be different.)
Mark
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 yes
#bottom_pbc yes
#average_pbc yes
top_area yes
bottom_area yes
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