# Error with "Distance between pull groups" and PBC for lipid bilayer and molecule interaction **URL:** \ **Category:** User discussions\ **Tags:** mdp-parameters\ **Created:** [May 29, 2023, 2:19pm UTC](https://gromacs.bioexcel.eu/t/error-with-distance-between-pull-groups-and-pbc-for-lipid-bilayer-and-molecule-interaction/6510 "2023-05-29T14:19:44Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![Brijesh](https://avatars.discourse-cdn.com/v4/letter/b/f475e1/32.png) [@Brijesh](https://gromacs.bioexcel.eu/u/Brijesh)\ **Post date:** [May 29, 2023, 2:19pm UTC](https://gromacs.bioexcel.eu/t/error-with-distance-between-pull-groups-and-pbc-for-lipid-bilayer-and-molecule-interaction/6510/1 "2023-05-29T14:19:45Z")
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](https://gromacs.bioexcel.eu/uploads/short-url/s6tgsucqbDrG8nXzvXZYyr1zQ8G.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](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/b/b3a36e2e972756b5dbf0a5b56fb125cf5538ecc0.png) Have a nice day Thanks and regards Brijesh ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [May 29, 2023, 7:02pm UTC](https://gromacs.bioexcel.eu/t/error-with-distance-between-pull-groups-and-pbc-for-lipid-bilayer-and-molecule-interaction/6510/2 "2023-05-29T19:02:48Z")
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. ---
**Author:** ![Brijesh](https://avatars.discourse-cdn.com/v4/letter/b/f475e1/32.png) [@Brijesh](https://gromacs.bioexcel.eu/u/Brijesh)\ **Post date:** [May 31, 2023, 5:49pm UTC](https://gromacs.bioexcel.eu/t/error-with-distance-between-pull-groups-and-pbc-for-lipid-bilayer-and-molecule-interaction/6510/3 "2023-05-31T17:49:16Z")
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 ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [June 2, 2023, 7:04am UTC](https://gromacs.bioexcel.eu/t/error-with-distance-between-pull-groups-and-pbc-for-lipid-bilayer-and-molecule-interaction/6510/4 "2023-06-02T07:04:39Z")
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? ---
**Author:** ![Brijesh](https://avatars.discourse-cdn.com/v4/letter/b/f475e1/32.png) [@Brijesh](https://gromacs.bioexcel.eu/u/Brijesh)\ **Post date:** [June 7, 2023, 7:22am UTC](https://gromacs.bioexcel.eu/t/error-with-distance-between-pull-groups-and-pbc-for-lipid-bilayer-and-molecule-interaction/6510/5 "2023-06-07T07:22:34Z")
Dear Hess, ```auto 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 ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [June 7, 2023, 11:15am UTC](https://gromacs.bioexcel.eu/t/error-with-distance-between-pull-groups-and-pbc-for-lipid-bilayer-and-molecule-interaction/6510/6 "2023-06-07T11:15:30Z")
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. ---
**Author:** ![Brijesh](https://avatars.discourse-cdn.com/v4/letter/b/f475e1/32.png) [@Brijesh](https://gromacs.bioexcel.eu/u/Brijesh)\ **Post date:** [June 8, 2023, 12:24pm UTC](https://gromacs.bioexcel.eu/t/error-with-distance-between-pull-groups-and-pbc-for-lipid-bilayer-and-molecule-interaction/6510/7 "2023-06-08T12:24:50Z")
Dear Hess, Thanks for the suggestion. I will try your suggestion and will update you. Have a great day Thanks and regards Brijesh