# Cross-linked polemer

**URL:** <https://gromacs.bioexcel.eu/t/cross-linked-polemer/7770>\
**Category:** User discussions\
**Created:** [December 1, 2023, 3:26pm UTC](https://gromacs.bioexcel.eu/t/cross-linked-polemer/7770 "2023-12-01T15:26:49Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![baharebamdad](https://avatars.discourse-cdn.com/v4/letter/b/9e8a1a/32.png) [@baharebamdad](https://gromacs.bioexcel.eu/u/baharebamdad)\
**Post date:** [December 1, 2023, 3:26pm UTC](https://gromacs.bioexcel.eu/t/cross-linked-polemer/7770/1 "2023-12-01T15:26:49Z")

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GROMACS version: 2019  
GROMACS modification: Yes/No  
Dear GROMACS people,

I am working with a complex cross-linked polymer and need to calculate the interaction between this polymer and a protein using Gromacs software. I have obtained the force field parameters (OPLS-AA) and the polymer-related topology file using Schrödinger software, and I converted them to a Gromacs-friendly format using [genTOP](https://github.com/sli259/genTOP).  
The issue arises during energy minimization, where the bonds between two rings in the polymer structure break, leading the system to exhibit a substantial potential energy on the order of 1E+8 kJ/mol. Could you please assist me in resolving this problem?

Best regards,  
Bahareh  
[mol.top](https://gromacs.bioexcel.eu/uploads/short-url/rrQXatGNLObYDiaT1p0YHNvXDzb.top) (5.5 MB)