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

[Justin Lemkul]

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 
system.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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