Kindly confirm whats the backend procedure to calculate membrane thickness in MEMBPLUGIN, is it the difference between the peaks in electron density profile for phosphates present in headgroups of the lipid.
According to my understanding membrane thickness must be the difference from electron density profile of separately two leaflets of the bilayers for the phosphates present in headgroups of the lipid. And also confirm that this membrane thickness is DHH membrane thickness (calculated for the phosphate atoms in the headgroups of the lipid)?
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
The (per-frame) thickness computation is based on the projected mass distributions for the selected atoms (usually "name P"). These projections should form two peaks; their distance is the membrane thickness, w(t). The algorithm is based on the first and second central moment of the mass distribution along Z axis (that is expected to be the bilayer normal):
R. Guixà-González; I. Rodríguez-Espigares; J. M. Ramírez-Anguita; P. Carrió-Gaspar; H. Martinez-Seara; T. Giorgino; J. Selent. MEMBPLUGIN: studying membrane complexity in VMD. Bioinformatics 2014; vol. 30 (10) p. 1478-1480 doi:10.1093/bioinformatics/btu037
so its not based on the selected atom P which comes from phosphate atoms
in lipid head groups and its not DHH (head to head separation based on
phosphates)... ?
On Thu, Jul 9, 2015 at 6:27 PM, Ismael Rodriguez Espigares
ismresp@users.sf.net wrote:
The (per-frame) thickness computation is based on the projected mass
distributions for the selected atoms (usually "name P"). These projections
should form two peaks; their distance is the membrane thickness, w(t). The
algorithm is based on the first and second central moment of the mass
distribution along Z axis (that is expected to be the bilayer normal):
R. Guixà-González; I. Rodríguez-Espigares; J. M. Ramírez-Anguita; P.
Carrió-Gaspar; H. Martinez-Seara; T. Giorgino; J. Selent. MEMBPLUGIN:
studying membrane complexity in VMD. Bioinformatics 2014; vol. 30 (10) p.
1478-1480 doi:10.1093/bioinformatics/btu037
Yes, it is. It is based only on "atom P" masses and distances. The equation applies only to the selection (phosphate atoms by default).
The average tab computes the average thickness in the whole selection, while thickness map computes the thickness along X and Y axis.
Just be careful that ONLY your lipids have the head phosphates named as "P" (as happens usually in CHARMM nomenclature) or change the default atomselection "name P" according to the nomenclature in your simulations.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Kindly confirm whats the backend procedure to calculate membrane thickness in MEMBPLUGIN, is it the difference between the peaks in electron density profile for phosphates present in headgroups of the lipid.
According to my understanding membrane thickness must be the difference from electron density profile of separately two leaflets of the bilayers for the phosphates present in headgroups of the lipid. And also confirm that this membrane thickness is DHH membrane thickness (calculated for the phosphate atoms in the headgroups of the lipid)?
The (per-frame) thickness computation is based on the projected mass distributions for the selected atoms (usually "name P"). These projections should form two peaks; their distance is the membrane thickness, w(t). The algorithm is based on the first and second central moment of the mass distribution along Z axis (that is expected to be the bilayer normal):
For more information, please check membrane thickness section at MEMBPLUGIN wiki and the paper:
Related
Wiki: Home
Wiki: MembraneThickness
Last edit: Ismael Rodriguez Espigares 2015-07-09
so its not based on the selected atom P which comes from phosphate atoms
in lipid head groups and its not DHH (head to head separation based on
phosphates)... ?
On Thu, Jul 9, 2015 at 6:27 PM, Ismael Rodriguez Espigares ismresp@users.sf.net wrote:
Yes, it is. It is based only on "atom P" masses and distances. The equation applies only to the selection (phosphate atoms by default).
The average tab computes the average thickness in the whole selection, while thickness map computes the thickness along X and Y axis.
Just be careful that ONLY your lipids have the head phosphates named as "P" (as happens usually in CHARMM nomenclature) or change the default atomselection "name P" according to the nomenclature in your simulations.