[gmx-users] Umbrella sampling

Justin Lemkul jalemkul at vt.edu
Wed Jan 22 22:18:32 CET 2014

On 1/22/14, 3:33 PM, Guo, Yanan wrote:
> 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?

I don't see why you would exclude H atoms from the selections.  If you want to 
do that, use make_ndx and type "help" at the prompt to see examples if you are 
unfamiliar with generating index groups.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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