Error with "Distance between pull groups" and PBC for lipid bilayer and molecule interaction

User discussions
1

GROMACS version:5.1.4
GROMACS modification: Yes/No
Dear GROMACS Users,
Can anyone help me with my problems pulling a molecule toward the lipid bilayer in MD simulation in GROMACS?
I am using the pull code from Prof Justin Lemkul in the Umbrella sampling tutorial using Gromacs as a reference for pulling a molecule towards the plasma membrane model.
md_pull.mdp (2.3 KB)

On using this command, I get
gmx grompp -f md_pull.mdp -c md_final.gro -p topol.top -r md_final.gro -n new.ndx -t md_final.cpt -o pull.tpr

I get an error stating: Can not have dynamic box while using pull geometry “direction-periodic” (dim z).

Screenshot from 2023-05-29 19-41-46
Screenshot from 2023-05-29 19-41-46709×579 64.4 KB

Have a nice day

Thanks and regards
Brijesh

2

Does Justins tutorial use geometry=distance-periodic?

Geometry distance-periodic is pulling molecules over distances of more than half the box and should almost never used. With a membrane one should use geometry=cylinder.

3

Dear Hess,

Thanks for replying
Prof. Lemkul uses pull_coord1_geometry = distance as given in the tutorial. I tried with this, but he pulls the protein chain there.
Here, I want to bring molecule towards the membrane. For this, I first gave pull_coord1_rate vale = -ve, which gave an error stating “When the maximum distance from a pull group reference atom to other atoms in the group is larger than 0.5 times half the box size a centrally placed atom should be chosen as pbc atom. Pull group 2 is larger than that and does not have a specific atom selected as reference atom”.

This same error comes when I use pull_coord1_geometry = distance and cylinder.

Have a nice day
Thanks and Regards
Brijesh

4

You would get that error with geometry=distance, but not with geometry=cylinder, if you chose the bilayer as the first group. Did you choose the bilayer as the first group?

5

Dear Hess,

pull                     = yes
pull-ncoords             = 1
pull-ngroups             = 2
pull-group1-name         = LIG
pull-group2-name         = DOPC_DOPG
pull-coord1-type         = umbrella
pull-coord1-geometry     = direction/cylinder
pull-coord1-dim          = N N Y
pull_coord1_vec          = 0.0 0.0 -1.0
pull-coord1-groups       = 1 2
pull-coord1_start        = yes
pull-coord1-rate         = -0.01
pull-coord1-k            = 1000.0

For pull-coord1-geometry, I used direction/distance/cylinder.
This works if I keep the box size at least 4 times of the distance between the molecule and the membrane.

Thanks for help

Have a nice day

Thanks and regards
Brijesh

6

You should use geometry=cylinder and swap the names of group 1 and 2. You might then also need to change the sign of the pull vector.

7

Dear Hess,

Thanks for the suggestion.
I will try your suggestion and will update you.

Have a great day

Thanks and regards
Brijesh