[gmx-users] No group in index file?

[Xu Dong Huang]

@ Justin,

That doesn’t sound very good. I tried it as he suggested using make_ndx, it seems to work, but it’s not reporting the result I want. When I use g_angle using the index i created, I chose the group I want to assess (My compound is very simple in Martini, it’s only represented by 3 atoms) and it reports back to me 1 angle value. However, I wish to assess the angle between atom 1 & 2, 2&3 and 1&3. How should I go about achieving that? 

Thanks,

Xu Huang

On Oct 31, 2013, at 4:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 
> 
> On 10/31/13 3:59 PM, Riccardo Concu wrote:
>> Dear Xu,
>> you have to use the make_ndx option if I'm not wrong.
>> The syntax should be make_ndx -f xxx.gro -o index.ndx
> 
> make_ndx is not particularly useful for angles.  To get it to recapitulate the function of mk_angndx, it's as much work as writing the index file by hand.
> 
> -Justin
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
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> University of Maryland, Baltimore
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> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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