[gmx-users] Angle group
jalemkul at vt.edu
Thu Jul 24 15:03:39 CEST 2014
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 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
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