[gmx-users] Angle group
jalemkul at vt.edu
Fri Jul 25 13:39:00 CEST 2014
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?
> 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 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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