Hi,
I am trying to use Membplugin for the membrane thickness analysis. My membrane deforms, bends/curves during simulation. When I calculate deformation map, it shows curved area to be thickest (almost double the average thickness of the membrane). Can you please help me with this. Thank you.
Sincerely,
Anjela
Hi Ismael,
I am calculating total thickness. When I calculate just the average
thickness, I am still getting high values (~166A) and thickness map (with
total thicknes) have similar values as well. Please let me know if more
information is required. Thank you.
Sincerely,
Anjela Manandhar
Graduate Student
Biochemistry Program
Graduate Center, City University of New York
365 Fifth Avenue, NY-10016, USA
our analysis (hence the code) assumes an “almost planar” bilayer. Yours is pretty strongly curved. What’s happening (as far as I can tell) is that the plane-fitting is failing and so is the upper/lower lipid assignment.
Maybe some future version…
Best
TG
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Thank you for the explanation Toni.
Sincerely,
Anjela Manandhar
Graduate Student
Biochemistry Program
Graduate Center, City University of New York
365 Fifth Avenue, NY-10016, USA
our analysis (hence the code) assumes an “almost planar” bilayer. Yours is
pretty strongly curved. What’s happening (as far as I can tell) is that the
plane-fitting is failing and so is the upper/lower lipid assignment.
Hi,
I am trying to use Membplugin for the membrane thickness analysis. My membrane deforms, bends/curves during simulation. When I calculate deformation map, it shows curved area to be thickest (almost double the average thickness of the membrane). Can you please help me with this. Thank you.
Sincerely,
Anjela
Dear Anjela,
In order to help you, could you tell me if you had computed the deformation map using the total thickness or the leaflet deformation option?
You can find our definition of leaflet deformation in [MembraneThickness] and how it is computed in this thread.
If you used the leaflet deformation option, the results look reasonable to me as the most deformed region of the membrane is the most curved region.
Best regards,
Ismael.
Related
Wiki: MembraneThickness
Last edit: Ismael Rodriguez Espigares 2019-07-25
Hi Ismael,
I am calculating total thickness. When I calculate just the average
thickness, I am still getting high values (~166A) and thickness map (with
total thicknes) have similar values as well. Please let me know if more
information is required. Thank you.
Sincerely,
Anjela Manandhar
Graduate Student
Biochemistry Program
Graduate Center, City University of New York
365 Fifth Avenue, NY-10016, USA
On Thu, Jul 25, 2019 at 5:19 PM Ismael Rodriguez Espigares ismresp@users.sourceforge.net wrote:
Related
Wiki: MembraneThickness
Dear Anjela,
our analysis (hence the code) assumes an “almost planar” bilayer. Yours is pretty strongly curved. What’s happening (as far as I can tell) is that the plane-fitting is failing and so is the upper/lower lipid assignment.
Maybe some future version…
Best
TG
Thank you for the explanation Toni.
Sincerely,
Anjela Manandhar
Graduate Student
Biochemistry Program
Graduate Center, City University of New York
365 Fifth Avenue, NY-10016, USA
On Mon, Jul 29, 2019 at 3:32 AM Toni tigio@users.sourceforge.net wrote: