Equilibration at MM and QMMM level using Amber and CPMD

This is a collection of tutorials that I wrote for myself. I find it convenient to go back here and read and update my workflow on the way. In this way I also keep track of what I did in the past and how I can improve it.

Note

Use at your own risk!

I am not an expert in everything written here! Some of the tutorials might contain commands and workflows that are not optimal at all or not recommended. If you have better ways of doing what I present here, or if you want to comment or share your own tricks, fell free to contact me.

Thanks!

For now the tutorials describe very short workflows that can be used to equilibrate systems with the Amber and CPMD packages. The material presented here is an adaptation and decomposition of a QM/MM tutorial by E. Ippoliti and J. Dreyer (Tutorial: QM/MM MD by CPMD).

• Generate RESP charges with Gaussian
• Generate .mol2 file for leap and Amber
• Leap (Amber): solvate molecule in TIP3P water
• Generate custom box with packmol
• Leap (Amber): set up a non-standard system from a .pdb file
• Leap (Amber): custom solvent box
• Amber: equilibrate system
• Run QM/MM calculations with CPMD