Pulling a group out of a membrane complex

User discussions
1

GROMACS version:2019.4
GROMACS modification: Yes/No
Here post your question
I am trying to run a simulation using the pull code to pull a peptide out of a membrane complex with which it is associated. I ahve tried several variations but keep having issues of the two groups that Iselect pulling and moving in opposite directions as opposed t oone of them moving and the other one remaining more or less where it is relative to the rest of the complex. The documentation for the pull code alludes to pulling with respect to he whole bilayer …but it doesn’t expand on how this would be done. I attach the most recent iteration of the pull code fro mmy mdp file below. Is there a simple setting that upon changing would fix my problem or a way of pulling the peptide out and counting on the strength of the interactions holding the rest of the complex in the bilayer?

pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull-pbc-ref-prev-step-com = yes
pull_group1_name = sub_end
pull_group2_name = ref
pull_group1_pbcatom = 7572
pull_group2_pbcatom = 12844
pull_coord1_vec = 0 0 -1
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = direction ; pull group away from reference group
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
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

Best

Matt

…

2

Hi,
I understand that you aim to pull a peptide (group 1=peptide) out of a lipid bilayer (reference group=lipids) along a direction defined by the pull_coord1_vec.
But I do fully not understand what is the problem with the results. Could you try to rephrase it?
Thank you
Alessandra

3

Dear alevilla,

Many thanks for getting back to me, I managed to solcve the issue, there was a typo in the MDP file, I had to change from isotropic to semi isotropic, change to cylinder geometry then it ran OK

4

Great!