Parameters for pulling through membrane

User discussions
1

GROMACS version: 2020.3
GROMACS modification: No

I’m trying to pull a molecule through a bilayer along the z-coordinate and at its start configuration, the COM of the molecule is 9 nm below the COM of the bilayer. How do I set a reference distance that’s beyond 0 nm (center of bilayer) so that I end up with the molecule 9 nm above the bilayer after pulling? Would I input a negative distance like -9.0 nm?

Thanks in advance!

2

You can controll the pull distance by adjusting pull speed and simulation time.

pull-coord1-geometry = direction
pull-coord1-vec = 0 0 1
pull-coord1-rate = 0.018

running with these parameters should yield a simulation in which the molecule is being pulled through the membrane in 1ns.
(you need to experiment with pull-coord1-k, start with some high value)

3

Thank you!