# Defining central atom in steered molecular dynamics

**URL:** <https://gromacs.bioexcel.eu/t/defining-central-atom-in-steered-molecular-dynamics/2531>\
**Category:** User discussions\
**Created:** [July 19, 2021, 5:37am UTC](https://gromacs.bioexcel.eu/t/defining-central-atom-in-steered-molecular-dynamics/2531 "2021-07-19T05:37:22Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![utkarsh](https://avatars.discourse-cdn.com/v4/letter/u/e9bcb4/32.png) [@utkarsh](https://gromacs.bioexcel.eu/u/utkarsh)\
**Post date:** [July 19, 2021, 5:37am UTC](https://gromacs.bioexcel.eu/t/defining-central-atom-in-steered-molecular-dynamics/2531/1 "2021-07-19T05:37:22Z")

</div>

GROMACS version:2021.1  
GROMACS modification: No  
Here post your question  
Hi,  
How to select the central atom of a protein for pulling? if remain unselected following error is displayed,  
**[error 1(file MDP/md\_pull.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 2 is larger than that & does not have a specific atom selected as reference atom.

**Details about the system:**  
System size: 4.950 9.590 7.930  
defined center: 3.0 5.5 4.0  
Box size: 20 11 10  
Pull-Dim: Y N N  
pull\_pbc\_ref\_prev\_step\_com = yes

Chain A: 50 residues  
Chain B: 539 residues

Position restrain on Chain A  
Pull rate: 0.001nm/ps  
Force: 1000 kJ/mol

Please share your inputs to rectify the error.

Thanks  
utk

---

<div class="post-metadata">

**Author:** ![pjohansson](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pjohansson/32/316_2.png) [@pjohansson](https://gromacs.bioexcel.eu/u/pjohansson)\
**Post date:** [July 19, 2021, 5:52am UTC](https://gromacs.bioexcel.eu/t/defining-central-atom-in-steered-molecular-dynamics/2531/2 "2021-07-19T05:52:51Z")

</div>

Hi,

specify your central atom index with `pull-group2-pbcatom = index` in the `.mdp` file. More information here: [Molecular dynamics parameters (.mdp options) — GROMACS 2021.2 documentation](https://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-pull-group1-pbcatom)

Regards,  
Petter

---

<div class="post-metadata">

**Author:** ![utkarsh](https://avatars.discourse-cdn.com/v4/letter/u/e9bcb4/32.png) [@utkarsh](https://gromacs.bioexcel.eu/u/utkarsh)\
**Post date:** [July 20, 2021, 6:13am UTC](https://gromacs.bioexcel.eu/t/defining-central-atom-in-steered-molecular-dynamics/2531/3 "2021-07-20T06:13:40Z")

</div>

Thanks petter, I was able to rectify the error.

Regards,  
utk

---

<div class="post-metadata">

**Author:** ![utkarsh](https://avatars.discourse-cdn.com/v4/letter/u/e9bcb4/32.png) [@utkarsh](https://gromacs.bioexcel.eu/u/utkarsh)\
**Post date:** [August 16, 2021, 7:58am UTC](https://gromacs.bioexcel.eu/t/defining-central-atom-in-steered-molecular-dynamics/2531/4 "2021-08-16T07:58:19Z")

</div>

Hi,  
While performing further simulation at different pH, for system at higher pH and pull in X-axis no need to define the **central atom** but at lower pH the same complex in X-axis pull shows an error to define an central atom.  
I am not able to understand this, Please help!  
Thanks