Choosing reaction coordinate in steered MD simulation to be a point in space

User discussions
1

GROMACS version: 2020.1-Ubuntu-2020.1-1
GROMACS modification: No
I am running a steered coarse-grained simulation of a peptide interacting with a bilayer, I am using the two reaction coordinates of the peptide’s COM and the bilayer COM, however to get a feel for how the force changes I would like to pull my peptide right through the bilayer onto the other side - I need to choose a reaction coordinate which is a certain coordinate point in my simulation space in my .mdp file - How can I do this?

Many thanks in advance!

Anna

2

I think you don’t want an absolute coordinate in space for that. You did not specify which reaction coordinate you are using, only which definition of the COMs or pull groups. For such studies you should use pull geometry cylinder.

3

Great thank you so much!

The simulation is running now :)