Steered MD simulation of ligand through membrane protein

GROMACS version: 2021
GROMACS modification: No
Hi everyone,

I am trying to perform a steered MD by pulling a ligand through a beta-barrel kind of membrane protein. As a starting configuration, I have put the ligand (a small cyclic sugar) on top of one of the openings of the beta-barrel protein and intend to pull the ligand through the protein along the z-direction (axis of the beta-barrel). So the protein is like a hollow cylinder with two openings: top and bottom (like a barrel made of beta sheets). I have made two separate index groups one for ligand and one for protein respectively. I am using the following pull-code settings:

; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = LIG
pull_group2_name = PROT
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = N N Y ; pull along z
pull_coord1_groups = 1 2 ; groups 1 (Chain A) and 2 (Chain B) define the reaction coordinate
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2

I am getting the following grompp error: “When the maximum distance from a pull group reference atom to other atomsin the group is larger than 0.5 times half the box size a centrally placed atom should be chosen as pbcatom. Pull group 2 is larger than that and does not have a specific atom selected as reference atom.”

I understand that this error refers to the fact that the beta-barrel protein diameter or distance from bottom to the top opening is larger than the half z-box vector. Since, this is a hollow cylinder looking protein (beta-barrel), there is no protein atom present at the center of geometry or center of mass that can be selected as pbcatom;

So my first question is: is there any other way or pull settings I can use to pull the ligand through the protein using protein-ligand distance as reaction coordinate

question-2: I have also tried to use the N-terminal C-alpha atom instead of the entire protein as a separate index group and tried to use center-center distance between N-term CA-LIG as reaction coordinate; In this case the pulling works and the ligand starts translocating through the protein; However the N-terminal part also starts to drift largely from its original positiona and once the ligand is very close to the N-term CA, the secondary structure changes (in the N-term region) from helix to coil---- which I think is not a right thing to happen;

So my second question is: is there a possibility where only the ligand will be pulled towards the protein not the N-term CA, so the secondary structure is conserved?

Thanks in advance

concerning the first questions, have you tried to use the mdp option pull-pbc-ref-prev-step-com together with pull-group?-pbcatom (see here Non-equilibrium pulling — GROMACS 2021.5 documentation)?

Concern the second questions, you can try to pull more gently (by changing k or rate). It can also be that the selected reaction coordinate is not the appropriate for your questions.

Kind regards

Hi, thank you very much alevilla, I have used an atom close to the center of the protein (chosen visually by looking at it in vmd) as pbcatom and now the pulling seems to work fine using the vector connecting com of ligand & com of protein as a reaction coordinate.