# How can I do MD simulation with Gromacs for a large protein?

**URL:** <https://gromacs.bioexcel.eu/t/how-can-i-do-md-simulation-with-gromacs-for-a-large-protein/819>\
**Category:** User discussions\
**Created:** [September 15, 2020, 7:28pm UTC](https://gromacs.bioexcel.eu/t/how-can-i-do-md-simulation-with-gromacs-for-a-large-protein/819 "2020-09-15T19:28:31Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![shokouhre](https://avatars.discourse-cdn.com/v4/letter/s/e47c2d/32.png) [@shokouhre](https://gromacs.bioexcel.eu/u/shokouhre)\
**Post date:** [September 15, 2020, 7:28pm UTC](https://gromacs.bioexcel.eu/t/how-can-i-do-md-simulation-with-gromacs-for-a-large-protein/819/1 "2020-09-15T19:28:32Z")

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GROMACS version:2020.2

Hello all  
How can I do MD simulation with Gromacs for a large protein (1300 aa)? Should I use the restrain file? If yes, how can I get the file?

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [September 15, 2020, 8:07pm UTC](https://gromacs.bioexcel.eu/t/how-can-i-do-md-simulation-with-gromacs-for-a-large-protein/819/2 "2020-09-15T20:07:20Z")

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The size of the protein doesn’t really impact the methods much. Restraints are typically employed during equilibration. You may want to work through some introductory tutorials (e.g. [http://www.mdtutorials.com/gmx/lysozyme/index.html](http://www.mdtutorials.com/gmx/lysozyme/index.html)) if these concepts aren’t familiar.

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**Author:** ![shokouhre](https://avatars.discourse-cdn.com/v4/letter/s/e47c2d/32.png) [@shokouhre](https://gromacs.bioexcel.eu/u/shokouhre)\
**Post date:** [September 15, 2020, 8:20pm UTC](https://gromacs.bioexcel.eu/t/how-can-i-do-md-simulation-with-gromacs-for-a-large-protein/819/3 "2020-09-15T20:20:44Z")

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> [@jalemkul](#):
>
> he size of the protein doesn’t really impact the methods much. Restraints are typically employed during equilibration. You may want to work through some introductory tutorials

Is it possible that the large size of the protein during simulation leads to its denaturation?

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [September 15, 2020, 8:38pm UTC](https://gromacs.bioexcel.eu/t/how-can-i-do-md-simulation-with-gromacs-for-a-large-protein/819/4 "2020-09-15T20:38:40Z")

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No, I would not think size alone would lead to denaturation.

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**Author:** ![shokouhre](https://avatars.discourse-cdn.com/v4/letter/s/e47c2d/32.png) [@shokouhre](https://gromacs.bioexcel.eu/u/shokouhre)\
**Post date:** [September 15, 2020, 8:41pm UTC](https://gromacs.bioexcel.eu/t/how-can-i-do-md-simulation-with-gromacs-for-a-large-protein/819/5 "2020-09-15T20:41:17Z")

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> [@jalemkul](#):
>
> not think size alone would lead to denatur

Thanks