# MD simulation of carbohydrates

**URL:** <https://gromacs.bioexcel.eu/t/md-simulation-of-carbohydrates/3273>\
**Category:** User discussions\
**Tags:** forcefield, mdp-parameters, mdrun\
**Created:** [December 9, 2021, 6:59am UTC](https://gromacs.bioexcel.eu/t/md-simulation-of-carbohydrates/3273 "2021-12-09T06:59:30Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Nupur\_Nagar](https://avatars.discourse-cdn.com/v4/letter/n/858c86/32.png) [@Nupur\_Nagar](https://gromacs.bioexcel.eu/u/Nupur_Nagar)\
**Post date:** [December 9, 2021, 6:59am UTC](https://gromacs.bioexcel.eu/t/md-simulation-of-carbohydrates/3273/1 "2021-12-09T06:59:30Z")

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GROMACS version: 2020.5  
GROMACS modification: Yes (gmx\_mpi)

Hi everyone

I want to check structural features of glycosaminoglycans (GAGs) and their interaction with small molecule through MD simulations. I read that GLYCAM06 FF is the suitable for running these simulations. However I am have trouble with the protocol and parameter files. Can anyone suggest a protocol for carbohydrate/ GAGs MD simulation which I can follow? It would be really helpful.

Thanks :)