GROMACS version: 2025.4
GROMACS modification: No
Hi all,
we are simulating the membrane insertion of a cyclic peptide (with a backbone diameter of 0.8 nm) into a lipid bilayer using AWH with cylinder pulling.
The initial geometry is:
- Z COM Peptide: 9.78 nm
- Z COM Membrane: 5.2 nm
- Z COM Lipids below peptide: 5.3 nm
Therefore, the expected distance between the peptide and the local membrane is approximately 4.5 nm. Since it was recommended at several posts in this forum, we would like to use the cylinder pull coordinate. However, we see strange results depending on the radius of the cylinder. We would assume naively that an increasing radius converges to the distance calculated with the direction pull coordinate. But apparently, it is vice versa. Did we understand it correctly that the first group in pull-coord1-groups must be the membrane?
| Geometry | pull-cylinder-r | Distance at start |
|---|---|---|
| cylinder | 5.0 nm | 1.178 nm |
| cylinder | 1.5 nm | 1.644 nm |
| cylinder | 0.1 nm | 4.130 nm |
| direction | -- | 4.482 nm |
Below I add the code for cylinder and radius. Why would this happen in the cylinder simulations?
#----------------------------------CYLINDER---------------------------
Radius 5.0 nm:
; Pull code
pull = yes
pull-ncoords = 1 ; only one reaction coordinate
pull-ngroups = 2 ; two groups defining one reaction coordinate
pull-group1-name = onlyMEMB ; pull towards membrane
pull-group2-name = LUGDBB ; pull the peptide COM
pull-coord1-type = external-potential ; Apply the bias using an external module.
pull-coord1-potential-provider = AWH ; The external module is called AWH!
pull-coord1-geometry = cylinder
pull-cylinder-r = see above
pull-coord1-dim = N N Y
pull-coord1-groups = 1 2
pull-coord1-vec = 0 0 -1 ; pull in z direction
pull-coord1-start = yes
pull-group1-pbcatom = 5902 ; roughly in the middle- took into account only for first step so not super-important
pull-pbc-ref-prev-step-com = yes ; the ref is adapted every step- necessary for large groups like membranes
#----------------------------------DIRECTION---------------------------
pull = yes
pull-ncoords = 1 ; only one reaction coordinate
pull-ngroups = 2 ; two groups defining one reaction coordinate
pull-group1-name = onlyMEMB ; pull towards lipid A phosphates
pull-group2-name = LUGDBB ; pull the peptide COM
pull-coord1-type = external-potential ; Apply the bias using an external module.
pull-coord1-potential-provider = AWH ; The external module is called AWH!
pull-coord1-geometry = direction
pull-coord1-dim = N N Y
pull-coord1-groups = 1 2
pull-coord1-vec = 0 0 -1 ; pull in z direction
pull-coord1-start = yes
pull-group1-pbcatom = 5902 ; roughly in the middle- took into account only for first step so not super-important
pull-pbc-ref-prev-step-com = yes ; the ref is adapted every step- necessary for large groups like membranes
Thanks a lot!