# Pulling simulations help

**URL:** <https://gromacs.bioexcel.eu/t/pulling-simulations-help/12252>\
**Category:** User discussions\
**Tags:** pull-code\
**Created:** [June 19, 2025, 10:26am UTC](https://gromacs.bioexcel.eu/t/pulling-simulations-help/12252 "2025-06-19T10:26:56Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![ghostpipierfish](https://avatars.discourse-cdn.com/v4/letter/g/71c47a/32.png) [@ghostpipierfish](https://gromacs.bioexcel.eu/u/ghostpipierfish)\
**Post date:** [June 19, 2025, 10:26am UTC](https://gromacs.bioexcel.eu/t/pulling-simulations-help/12252/1 "2025-06-19T10:26:56Z")

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GROMACS version: 2019.3/intel-2018  
GROMACS modification: No

Hi,

I’m trying to do a simple pulling simulation in the z direction. I’ve decided to put a position restraint on the N terminus of my protein (the entire first residue) and pull on the C terminus (the full last residue). Here is my pull code.

; Pull code  
pull = yes  
pull\_ncoords = 1 ; only one reaction coordinate  
pull\_ngroups = 2 ; two groups defining one reaction coordinate  
pull\_group1\_name = Chain\_A  
pull\_group2\_name = Chain\_B  
pull\_coord1\_type = umbrella ; harmonic potential  
pull\_coord1\_geometry = distance ; simple distance increase  
pull\_coord1\_dim = N N Y  
pull\_coord1\_groups = 1 2  
pull\_coord1\_start = yes ; define initial COM distance \> 0  
pull\_coord1\_rate = 0.001 ; 0.01 nm per ps = 10 nm per ns  
pull\_coord1\_k = 1000 ; kJ mol^-1 nm^-2  
pull\_group1\_pbcatom = 1957 (mid atom number of the last residue)  
pull\_pbc\_ref\_prev\_step\_com = yes

Looking at my pullf.xvg file, I can’t interpret where I’ve gone wrong.

 ![Screenshot 2025-06-19 at 11.25.24](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/d/dc41c0c80a362689e225a55c1b2a76271fcf6d21.png)

Looking at my trajectory in VMD, it looks like both ends of my protein is being pulled?

 ![Screenshot 2025-06-19 at 11.26.22](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/d/d50cb11de9c16c82a8187879ffb411267c015f42.png)

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<div class="post-metadata">

**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\
**Post date:** [June 28, 2025, 4:50am UTC](https://gromacs.bioexcel.eu/t/pulling-simulations-help/12252/2 "2025-06-28T04:50:03Z")

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Is the issue here that both chains are unraveling? I don’t think that’s an error, if you pull on the C-terminus and the helices are strongly bound together then it makes sense that the helix on the side of the restrained terminus would also be pulled apart as the helices are pulling on each other