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

User discussions
1

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?

2

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) if these concepts aren’t familiar.

3

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

4

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

5

Thanks