I see your confusion now.
The PMF is actually defined as dG(x) + C, where C is some unknown constant.
Therefore, in the left figure, you have dG_a(x) + C_a and on the right you
have dG_b(x) + C_b, so if the profiles have the same shape then the PMFs can
be identical if C_a is different from
Can you walk me through that image and tell me what you see that is different
from what you expect? I see a maximum at z=0 in both cases (I presume z=0 is
the bilayer center). I'm happy to continue guessing, but you are really best to
take something like hexane in a simplified bilayer and do a
Better yet, repeat something that is already out there in the literature. PMFs
for water, lipids, and some amino acid side chains across the bilayer have been
tested extensively.
Chris.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
Thanks Chris for your help
I am using Isoniazid drug and the membrane model is a mixture of different
lipid types (POPE,POPC,POPI,POPS,cholesterol) in a ratio mimicking the plasma
membrane more closely as compared to the simple single lipid type membrane
model. I have attached the PMF
Take a look at profiles in the literature for arginine across a bilayer. It has
a maximum at the center. Probably true for any molecule with a large
charge/molecular weight ratio. For more help you'd likely have to reveal your
system and provide an image of the PMF. However, there is no reason
