GROMACS version: 2021.4-Ubuntu-2021.4-2
GROMACS modification: No
I tried to perform energy minimization using the link here “Lysozyme in Water”.
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”.
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!
