[gmx-users] Angle group

[Justin Lemkul]

On 7/24/14, 8:55 AM, Cyrus Djahedi wrote:
> I tried using g_angle with an index file defining the three atoms that make up the bond as "Group    12 (       O1_C1_C4) has   960 elements". I get:
>
> Group     0 (         System) has 27396 elements
> Group     1 (          Other) has  6768 elements
> Group     2 (           GL4b) has   352 elements
> Group     3 (           G14b) has  6048 elements
> Group     4 (           GL1b) has   368 elements
> Group     5 (          Water) has 20628 elements
> Group     6 (            SOL) has 20628 elements
> Group     7 (      non-Water) has  6768 elements
> Group     8 (             O1) has   320 elements
> Group     9 (             O4) has    16 elements
> Group    10 (             C1) has   320 elements
> Group    11 (             C4) has   320 elements
> Group    12 (       O1_C1_C4) has   960 elements
> Group    13 (       C1_O1_C4) has   960 elements
> Group    14 (       C4_C1_O1) has   960 elements
> Group    15 (       C1_C4_O1) has   960 elements
> Group    16 (       O1_C1_C4) has   960 elements
> Select a group: 12
> Selected 12: 'O1_C1_C4'
> Last frame      10000 time 10000.000
> Found points in the range from 5 to 43 (max 180)
>   < angle >  = 23.1856
> < angle^2 > = 537.601
> Std. Dev.   = 0.170041
>
> I dont know exactly what angle it is referring to. The angle I'm looking for is formed at the O1-atom, flanked by the carbon atoms and is around 118-120 degrees . As you can see in the index-options I tried defining the triplets in different order, this made no difference however. Any suggestions?
>

The values printed are an average over all triplets in the chosen index group. 
I would think that order would absolutely matter here; check carefully how you 
have created the groups.  The angle formed by C1-O1-C4 must be different than 
the angle of O1-C1-C4.

-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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