# Calculating the distance between fixed point and a particle and warning about absolute reference

**URL:** <https://gromacs.bioexcel.eu/t/calculating-the-distance-between-fixed-point-and-a-particle-and-warning-about-absolute-reference/930>\
**Category:** User discussions\
**Created:** [October 7, 2020, 7:15pm UTC](https://gromacs.bioexcel.eu/t/calculating-the-distance-between-fixed-point-and-a-particle-and-warning-about-absolute-reference/930 "2020-10-07T19:15:32Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![nasrola\_hayati](https://avatars.discourse-cdn.com/v4/letter/n/46a35a/32.png) [@nasrola\_hayati](https://gromacs.bioexcel.eu/u/nasrola_hayati)\
**Post date:** [October 7, 2020, 7:15pm UTC](https://gromacs.bioexcel.eu/t/calculating-the-distance-between-fixed-point-and-a-particle-and-warning-about-absolute-reference/930/1 "2020-10-07T19:15:32Z")

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GROMACS version: 2019  
GROMACS modification: Yes/No  
Hi  
I was pulling a particle to a fixed point in the simulation box. but it didn’t work.  
Here’s its error:

WARNING 1 [file md\_pull.mdp]:  
You are using an absolute reference for pulling, but the rest of the  
system does not have an absolute reference. This will lead to artifacts.

How can I fix it?

Another question is about calculating the distance between fixed point and a particle (\< groups.txt &\>/dev/null is applicable for two groups).

pull = yespull-ncoords = 1  
pull-group1-name = VO  
pull-coord1-type = umbrella ;constant-force  
pull-coord1-geometry = direction  
pull-coord1-dim = N N Y  
pull-coord1-vec = 0.0 0.0 1.0  
pull-coord1-origin = 5 5 10  
pull-coord1-start = yes  
pull-coord1-rate = 0.01  
pull-coord1-k = 1000  
pull-coord1-groups = 0 1

How should I do that?

best regard  
nasrolla

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<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:** [October 12, 2020, 8:33am UTC](https://gromacs.bioexcel.eu/t/calculating-the-distance-between-fixed-point-and-a-particle-and-warning-about-absolute-reference/930/2 "2020-10-12T08:33:46Z")

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Hi,  
here two posts on similar issue.

> [@MD file error](https://gromacs.bioexcel.eu/t/md-file-error/891):
>
> GROMACS version: 2020.1 GROMACS modification: Yes/No Hi , there I wanted to pull a ligand out of the protein-ligand complex in the z-axis determined by fast pulling ligand method. But encountered an error during the run like this: ERROR 1 [file md.mdp]: 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 pbcatom. Pull group 1 is larger than that and does not have a sp…

and

> [@COM pulling](https://gromacs.bioexcel.eu/t/com-pulling/783):
>
> GROMACS version: 2018 GROMACS modification: No Dear all, I am looking for a way to restrain the center of mass (COM) of two different molecules bathed in water. The only thing close I found on gromacs that does this is the pull module embedded in the mdp files. I want to clarify that I want to restrain each molecules (COM) to a different and specific coordinate in my simulated box. Indeed the pull module has an option - pull-coord1-geometry = direction, where I can set the origin (pull-coor…

best regards  
Alessandra