[gmx-users] Umbrella sampling

Guo, Yanan yanan.guo at partner.kit.edu
Wed Jan 22 21:33:29 CET 2014

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!



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