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.
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