[gmx-users] groups selection make_ndx -f npt.gro

Justin Lemkul jalemkul at vt.edu
Fri May 10 11:58:05 CEST 2013

On 5/10/13 12:35 AM, Arunima Shilpi wrote:
> Hello sir
> As in the tutorial for umbrella sampling command
> make_ndx -f npt.gro
> you have selected two different groups as Chain_A as 19 and Chain_B as 20
> If we have protein-ligand interaction whether we should have single group
> of protein-ligand complex or we should use two different groups for protein
> and ligand.

A single group makes no sense.  Consider what chains A and B are in the tutorial 
- the pulled and reference groups, respectively.  Apply the same logic in your 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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