Hello,
In the system, I have 7 polymers. They are separated and curved to form a belt around the DMPC.
I’m trying to apply a flat-bottom cylindrical restraint in GROMACS (v2024.4) to keep the polymers close to a DMPC nanodisc in the XY-plane and create a belt-like arrangement around the nanodisc.
I aim to apply the restraint for a short period (a few nanoseconds), observe the interaction between the polymer and the membrane, and then release the restraint.
Both the polymer and the nanodisc lie in the XY-plane.
Here is the relevant part of my .mdp file:
pull = yes
pull_ngroups = 2
pull_ncoords = 1
pull_group1_name = DMPC
pull_group2_name = chain1
pull_coord1_type = flat-bottom
pull_coord1_geometry = cylinder
pull_coord1_dim = Y Y N
pull_coord1_groups = 1 2
pull_coord1_k = 15000
pull_coord1_rate = 0.0
pull_coord1_start = yes
pull-pbc-ref-prev-step-com = yes
pull_group1_pbcatom = 14501 ; selected atom near the center of the DMPC disc
pull_group2_pbcatom = 135 ; selected atom near the center of chain1
pull_coord1_vec = 1 1 0
Questions:
1)Does the setup above apply a flat-bottom cylindrical restraint to keep the polymer in the XY-plane?
- Is there any recommended way to keep the polymer wrapped around the DMPC like a belt, just for a while?
Thank you so much for your help and advice!
Best regards,
Fatemeh