[gmx-users] Umbrella sampling

[Guo, Yanan]

Dear gmx-users:



My system is a protein-ligand complex. I want to perform umbrella sampling calculation on the complex. The ligand is the group to which pulling force is applied. I chose five residues (r 192-196)of the protein as the reference group for pulling.



So firstly I need to define two index groups for the pulling system. My question is that do I need to define LIG-H and Ref_Group-H (-H means without hydrogen atoms), or just LIG and Ref_Group (with hydrogen atoms)?  And Why?  If it is the former case, what is the command to define the LIG-H and Ref_Group-H index groups?



Any suggestion and help will be appreciated. Thank you!



Best

Yanan