# Pulling a group out of a membrane complex

**URL:** <https://gromacs.bioexcel.eu/t/pulling-a-group-out-of-a-membrane-complex/1038>\
**Category:** User discussions\
**Created:** [November 2, 2020, 9:48pm UTC](https://gromacs.bioexcel.eu/t/pulling-a-group-out-of-a-membrane-complex/1038 "2020-11-02T21:48:52Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![mattyboi](https://avatars.discourse-cdn.com/v4/letter/m/85f322/32.png) [@mattyboi](https://gromacs.bioexcel.eu/u/mattyboi)\
**Post date:** [November 2, 2020, 9:48pm UTC](https://gromacs.bioexcel.eu/t/pulling-a-group-out-of-a-membrane-complex/1038/1 "2020-11-02T21:48:52Z")

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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

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [November 6, 2020, 9:03am UTC](https://gromacs.bioexcel.eu/t/pulling-a-group-out-of-a-membrane-complex/1038/2 "2020-11-06T09:03:43Z")

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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

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**Author:** ![mattyboi](https://avatars.discourse-cdn.com/v4/letter/m/85f322/32.png) [@mattyboi](https://gromacs.bioexcel.eu/u/mattyboi)\
**Post date:** [November 6, 2020, 9:36am UTC](https://gromacs.bioexcel.eu/t/pulling-a-group-out-of-a-membrane-complex/1038/3 "2020-11-06T09:36:04Z")

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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

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [November 6, 2020, 9:41am UTC](https://gromacs.bioexcel.eu/t/pulling-a-group-out-of-a-membrane-complex/1038/4 "2020-11-06T09:41:53Z")

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Great!