# High LJ (SR) in graphene sheet minimization

**URL:** https://gromacs.bioexcel.eu/t/high-lj-sr-in-graphene-sheet-minimization/12447
**Category:** User discussions
**Tags:** mdrun, simulation-setup
**Created:** [July 28, 2025, 5:26am UTC](https://gromacs.bioexcel.eu/t/high-lj-sr-in-graphene-sheet-minimization/12447 "2025-07-28T05:26:09Z")
**Posts on this page:** 1
**Page:** 1

<div class="post-metadata">

### Author: ![abhiram](https://avatars.discourse-cdn.com/v4/letter/a/43a26b/32.png) [@abhiram](https://gromacs.bioexcel.eu/u/abhiram)
#### Post date: [July 28, 2025, 5:26am UTC](https://gromacs.bioexcel.eu/t/high-lj-sr-in-graphene-sheet-minimization/12447/1 "2025-07-28T05:26:09Z")

</div>

I have tried to simulate graphene - water interaction using gromacs. I generated the itp file using the tutorial attached:

> **[Graphene Set Up](https://www.erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/)**
>
> Example Protocol: Graphene Sheet in Water This example has been kindly provided by Shansi Thian.   1. Create a new working directory GRAPHENE. Copy charmm36.ff forcefield file into it.   …

But I am obtaining a very high LJ (SR) potential on minimization and even in equilibriation (order of 1e+06). I have taken care of pbc in x and y and I have given sufficient vacuum in z to avoid interaction with the periodic images. May i please know the issue to troubleshoot?

I have verified the number of bonds to be correct based on the number of atoms also.