# I tried to perform energy minimization using "http://www.mdtutorials.com/gmx/lysozyme/05\_EM.html"

**URL:** <https://gromacs.bioexcel.eu/t/i-tried-to-perform-energy-minimization-using-http-www-mdtutorials-com-gmx-lysozyme-05-em-html/10287>\
**Category:** User discussions\
**Tags:** simulation-setup, energy-minization\
**Created:** [October 5, 2024, 8:16am UTC](https://gromacs.bioexcel.eu/t/i-tried-to-perform-energy-minimization-using-http-www-mdtutorials-com-gmx-lysozyme-05-em-html/10287 "2024-10-05T08:16:38Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![pratikkhanal](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pratikkhanal/32/3856_2.png) [@pratikkhanal](https://gromacs.bioexcel.eu/u/pratikkhanal)\
**Post date:** [October 5, 2024, 8:16am UTC](https://gromacs.bioexcel.eu/t/i-tried-to-perform-energy-minimization-using-http-www-mdtutorials-com-gmx-lysozyme-05-em-html/10287/1 "2024-10-05T08:16:38Z")

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GROMACS version: 2021.4-Ubuntu-2021.4-2  
GROMACS modification: No

I tried to perform energy minimization using the link here “[Lysozyme in Water](http://www.mdtutorials.com/gmx/lysozyme/05_EM.html)”.  
But there is no mention of how to create the minim.mdp file. Also I am encountering frequent issue with error message (“number of coordinates in coordinate file does not match topology”.

 ![Capture](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/c/ca2173d640e410acadab847ee1ceac37c7f0050d.jpeg)

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**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\
**Post date:** [October 5, 2024, 4:28pm UTC](https://gromacs.bioexcel.eu/t/i-tried-to-perform-energy-minimization-using-http-www-mdtutorials-com-gmx-lysozyme-05-em-html/10287/2 "2024-10-05T16:28:07Z")

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Dear @pratikkhanal

the `minim.mdp` file is reported in the line before the `gmx grompp` command, just click on the red word **this** and copy paste the lines you find inside into a `minim.mdp` text file that you can generate with whatever text editor you like.

The “Number of coordinates…” error is a typical error that occurs when the contents of the structure file (.gro/.pdb etc.) do not correspond to the content of the topology (.top) file. It’s a rather common error when you are building a system from scratch, especially if this is your first time with GROMACS. Just try to go through the passages again and try to understand how the topology works within GROMACS!