# Pulling in non-rectangular box

**URL:** <https://gromacs.bioexcel.eu/t/pulling-in-non-rectangular-box/1121>\
**Category:** User discussions\
**Created:** [November 19, 2020, 4:04pm UTC](https://gromacs.bioexcel.eu/t/pulling-in-non-rectangular-box/1121 "2020-11-19T16:04:55Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![StefanS](https://avatars.discourse-cdn.com/v4/letter/s/9d8465/32.png) [@StefanS](https://gromacs.bioexcel.eu/u/StefanS)\
**Post date:** [November 19, 2020, 4:04pm UTC](https://gromacs.bioexcel.eu/t/pulling-in-non-rectangular-box/1121/1 "2020-11-19T16:04:55Z")

</div>

GROMACS version: 2020.3, 2020.0, 2018.8  
GROMACS modification: No  
Dear Gromacs Users,

I encountered an issue when trying to use constant velocity pulling with the gmx pull code with a membrane system with a hexagonal shape.  
**Initial structure/system:**  
Transmembrane protein in hexagonal membrane patch, 136826 atoms, centered so that k97 (pull-group1) is centered in the box with trjconv -ur compact -pbc mol -center. This should also put the center of mass of the membrane close to the center of the box.  
Dimensions (last line of .gro file): 11.26904 9.75928 12.10227 0.00000 0.00000 -5.63452 0.00000 0.00000 0.00000

**What I try to do:**  
Pull k97 in x direction (ultimately I want to pull in all three directions, but only the x direction causes problems) while holding the membrane stable.

pull = yes  
pull-ncoords = 1  
pull-ngroups = 2  
pull-group1-name = k97 ;; specific lysine that I want to pull at  
pull-group2-name = MEMB ;; whole membrane  
pull-group2-pbcatom = 25084 ;; arbitrary membrane atom relatively close to the center of the box  
pull-pbc-ref-prev-step-com = yes  
pull-coord1-groups = 1 2  
pull-coord1-type = umbrella  
pull-coord1-geometry = direction  
pull-coord1-vec = -1 0 0  
pull-coord1-dim = Y N N  
pull-coord1-rate = 0.3 ;; fast, just for testing  
pull-coord1-k = 10 ;; kJ mol^-1 nm^-2  
pull-coord1-start = no

**Problem:**  
gmx grompp does not complain about this, but when I start my simulation, gmx mdrun crashes at the first step with this error message:  
“Fatal error:  
Distance between pull groups 1 and 2 (4.842380 nm) is larger than 0.49 times  
the box size (4.782055).  
You might want to consider using “pull-geometry = direction-periodic” instead.”

The initial distance should not be that large and also the x box size mdrun returns is much smaller than the one in the gro file.

Am I overseeing anything? Has anyone encountered similar issues?

Many thanks,  
Stefan

---

<div class="post-metadata">

**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 20, 2020, 10:16am UTC](https://gromacs.bioexcel.eu/t/pulling-in-non-rectangular-box/1121/2 "2020-11-20T10:16:12Z")

</div>

Hi,  
what about to use `pull-coord-geometry = cylinder`?  
That is what works best for pulling a lipid from a membrane layer  
(see [http://manual.gromacs.org/current/reference-manual/special/pulling.html?highlight=definition%20center%20mass](http://manual.gromacs.org/current/reference-manual/special/pulling.html?highlight=definition%20center%20mass)).

Best regard  
Alessandra

---

<div class="post-metadata">

**Author:** ![StefanS](https://avatars.discourse-cdn.com/v4/letter/s/9d8465/32.png) [@StefanS](https://gromacs.bioexcel.eu/u/StefanS)\
**Post date:** [November 23, 2020, 10:08am UTC](https://gromacs.bioexcel.eu/t/pulling-in-non-rectangular-box/1121/3 "2020-11-23T10:08:11Z")

</div>

Hi Alessandra,

thank you very much for your suggestion!  
I only got around to testing it now - unfortunately the cylindrical geometry doesn’t work either…

Cheers,  
Stefan