# Diversity in minimal periodic distance in different 200-ns MD simulations

**URL:** <https://gromacs.bioexcel.eu/t/diversity-in-minimal-periodic-distance-in-different-200-ns-md-simulations/7828>\
**Category:** User discussions\
**Created:** [December 9, 2023, 10:05am UTC](https://gromacs.bioexcel.eu/t/diversity-in-minimal-periodic-distance-in-different-200-ns-md-simulations/7828 "2023-12-09T10:05:02Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![farial.t](https://avatars.discourse-cdn.com/v4/letter/f/ccd318/32.png) [@farial.t](https://gromacs.bioexcel.eu/u/farial.t)\
**Post date:** [December 9, 2023, 10:05am UTC](https://gromacs.bioexcel.eu/t/diversity-in-minimal-periodic-distance-in-different-200-ns-md-simulations/7828/1 "2023-12-09T10:05:02Z")

</div>

GROMACS version: 2022.4  
GROMACS modification: Yes/No no  
Here post your question  
Dear GROMACS users

I have completed a protein (WT & mutant) simulation for 200 ns in triplicates using Amber99sb force filed and TIP3P water model. I have used both cubic and dodecahedron boxes with a distance of 1.0 nm from the box edges (-d 1.0) in differenet runs. The vdw cut-off is set to 1.2 nm (rvdw =1.2) and long-range electrostatic cut-off is set to 1.2 nm (rcoulomb=1.2). Now I am interested in analysing the minimal periodic distance using gmx mindist module of GROMACS to check whether the protein has seen its periodic image during the simulation.  
The used command:  
gmx mindist -s .tpr -f nopbc.xtc -od minimal\_periodic\_dist.xvg -pi  
then the protein was selected.  
The results for the first run and the second run with a cubic box were respectively:  
The shortest periodic distance is 2.15047 (nm) at time 144990 (ps) and the shortest periodic distance is 2.1 nm at 163585 ps.  
But the result for the third run with a dodecahedron box was lower than 2 nm:  
The shortest periodic distance is 1.74 nm at 22800 ps.  
In addition, the shortest periodic distance for the mutant protein in the first run with a cubic box was 2.09 at 113866 ps while it was 1.8 nm at 420.168 ps in the second run with the same box.  
I don’t know why the minimal periodic distance has been changed to lower than 2 nm in different 200-ns MD simulations. My question is how can I interpret the results of gmx mindist according to my system?

Thanks in advance  
Farial Tavakoli

---

<div class="post-metadata">

**Author:** ![milosz.wieczor](https://avatars.discourse-cdn.com/v4/letter/m/b19c9b/32.png) [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\
**Post date:** [December 10, 2023, 8:13pm UTC](https://gromacs.bioexcel.eu/t/diversity-in-minimal-periodic-distance-in-different-200-ns-md-simulations/7828/2 "2023-12-10T20:13:40Z")

</div>

Proteins are flexible, and the difference between a value of 2.15 nm and 1.74 nm can be one between a slightly more extended and more compact conformation of a loop. It’s not great to have the minimal distance lower than 2 nm, but it’s not terrible either (check out a great discussion of box-size effects [here](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7481008/)), and overall it’s nothing surprising if you know that proteins can be non-spherical and change shape over time.