# Pulling two CG lipid vesicles toward each other

**URL:** <https://gromacs.bioexcel.eu/t/pulling-two-cg-lipid-vesicles-toward-each-other/9010>\
**Category:** User discussions\
**Tags:** simulation-setup\
**Created:** [April 29, 2024, 12:14am UTC](https://gromacs.bioexcel.eu/t/pulling-two-cg-lipid-vesicles-toward-each-other/9010 "2024-04-29T00:14:38Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![sunnytov](https://avatars.discourse-cdn.com/v4/letter/s/bc8723/32.png) [@sunnytov](https://gromacs.bioexcel.eu/u/sunnytov)\
**Post date:** [April 29, 2024, 12:14am UTC](https://gromacs.bioexcel.eu/t/pulling-two-cg-lipid-vesicles-toward-each-other/9010/1 "2024-04-29T00:14:38Z")

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GROMACS version:2023.3  
GROMACS modification: Yes/No  
Here post your question

Hello All

I am trying to pull two large CG vesicles that are aligned along the X axis from 51 nm distance to 1 nm. Below is the MDP options I used, which worked for another system.

* * *

; COM PULLING  
pull = yes  
; Cylinder radius for dynamic reaction force groups (nm)  
pull-cylinder-r = 1.5  
pull-constr-tol = 1e-06  
pull-print-com = yes  
pull-print-ref-value = no  
pull-print-components = no  
pull-nstxout = 50  
pull-nstfout = 50  
pull-pbc-ref-prev-step-com = yes  
pull-xout-average = no  
pull-fout-average = no  
; Number of pull groups  
pull-ngroups = 2  
; Number of pull coordinates  
pull-ncoords = 1  
; Group and coordinate parameters  
pull-group1-name = ves1 ;lipids and water and ions inside of the left vesicle  
pull-group2-name = ves2 ; lipids and water and ions inside of the right vesicle  
pull-group1-weights =  
pull-group1-pbcatom = 542874  
pull-group2-pbcatom = 1920406  
pull-coord1-type = constant-force  
pull-coord1-potential-provider =  
pull-coord1-expression =  
pull-coord1-dx = 1e-09  
pull-coord1-geometry = distance  
pull-coord1-groups = 1 2  
pull-coord1-dim = Y N N  
pull-coord1-start = yes  
pull-coord1-init =  
pull-coord1-rate = 0.001 ; 0.001nm per ps = 1 nm per 1 ns  
pull-coord1-k = 1000 ; KJ mol-1 nm -1  
pull-coord1-kB = 0

* * *

This set up worked for a similar system but it fails for the current one with this following error message.

* * *

## Note that mdrun will redetermine rlist based on the actual pair-list setup Pull group natoms pbc atom distance at start reference at t=0 1 340857 542874 2 343395 1920406

Program: gmx grompp, version 2023.3  
Source file: src/gromacs/pulling/pull.cpp (line 525)

Fatal error:  
Distance between pull groups 1 and 2 (51.721501 nm) is larger than 0.49 times  
the box size (50.828498).

* * *

The box sizes are 103.73163 51.86582 51.86582, and hence the X axis is clearly longer than the starting COM distance.

Could you tell me how to change the parameters to resolve the error?

Thanks in advance

Sunjoo

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<div class="post-metadata">

**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:** [April 29, 2024, 8:38am UTC](https://gromacs.bioexcel.eu/t/pulling-two-cg-lipid-vesicles-toward-each-other/9010/2 "2024-04-29T08:38:05Z")

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You have to use geometry=direction for this.

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<div class="post-metadata">

**Author:** ![sunnytov](https://avatars.discourse-cdn.com/v4/letter/s/bc8723/32.png) [@sunnytov](https://gromacs.bioexcel.eu/u/sunnytov)\
**Post date:** [April 29, 2024, 12:24pm UTC](https://gromacs.bioexcel.eu/t/pulling-two-cg-lipid-vesicles-toward-each-other/9010/3 "2024-04-29T12:24:56Z")

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Thanks!  
I will try

Sunjoo