[gmx-users] Angle group

[Justin Lemkul]

On 7/25/14, 7:35 AM, Cyrus Djahedi wrote:
> There is something else. I also tried using mk_angndx to generate an index file prior to using g_angle by: "mk_angndx -s C0.tpr -type angle"
> It generates a lot of different angle group that I can not identify. Each line in the index-file has 9 atoms in it, are the atoms divided three-by-three to form a triplet? Is there any way of knowing which group represents which triplet?
>
> g_angle:
>
> Group     0 (Theta=110.0_502.42) has  7680 elements
> Group     1 (Theta=111.0_376.81) has 10560 elements
> Group     2 (Theta=112.0_837.36) has   960 elements
> Group     3 (Theta=107.5_586.15) has  4944 elements
> Group     4 (Theta=108.5_586.15) has  5616 elements
> Group     5 (Theta=109.5_460.55) has  2976 elements
> Group     6 (Theta=113.5_376.81) has  3840 elements
> Group     7 (Theta=111.6_418.68) has  1872 elements
> Group     8 (Theta=109.5_376.81) has   960 elements
> Select a group: 2
> Selected 2: 'Theta=112.0_837.36'
> Last frame      10000 time 10000.000
> Found points in the range from 93 to 124 (max 180)
>   < angle >  = 108.363
> < angle^2 > = 11742.5
> Std. Dev.   = 0.214073
>

mk_angndx divides the groups based on their parameters, not necessarily by the 
same chemical definition (i.e. the same bonded parameters may apply to different 
groups in your structure).  You can always identify what the groups contain by 
opening the .ndx file in a text editor; all an .ndx file has is a list of atom 
numbers, so it's easy to tell what is what.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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