[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

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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