AW: [gmx-users] Have read the manual => How to calculate dihedral angle??????

[serdar durdagi]

Why you don't want to use VMD program? It's very easy to get dihedral angles from there.
 
serdar

--- Chih-Ying Lin <chihying2008 at gmail.com> schrieb am Mi, 2.7.2008:

Von: Chih-Ying Lin <chihying2008 at gmail.com>
Betreff: [gmx-users] Have read the manual => How to calculate dihedral angle??????
An: gmx-users at gromacs.org
Datum: Mittwoch, 2. Juli 2008, 7:42

HI
I have read the manual  but the thing is that I could not get the
answers from the manuals.  So, I repeatly ask the same questions and
if anyone could give me the exact answers. Thanks a lot.

Lin




I use   mk_angndx   to     produce      angle.ndx
then, enter  g_angle -od angdist.xvg -ov angaver.xvg -type dihedral


it follows the options:
Group     0 (Phi=180.0_2_70) has     4 elements
Group     1 (Phi=180.0_2_6) has    16 elements
Group     2 (Phi=180.0_2_40) has   192 elements
Select a group:


what does the file angle.ndx mean?
what are the three groups represent ?
which group should I pick up?



this is the angle.ndx
what does it mean??
[ Phi=180.0_2_70 ]
   11    12    13    14
[ Phi=180.0_2_6 ]
    7    11    12    13     9    11    12    13    12    13    14    15
   12    13    14    17
[ Phi=180.0_2_40 ]
    2     1     3     4     2     1     3     7     5     1     3     4
    5     1     3     7     4     3     7     8     1     3     7     8
    1     3     7    11     4     3     7    11     8     7    11    12
    3     7    11     9     8     7    11     9     3     7    11    12
    7    11     9     5     7    11     9    10    12    11     9     5
   12    11     9    10    11     9     5     1    11     9     5     6
   10     9     5     1    10     9     5     6     9     5     1     3
    9     5     1     2     6     5     1     3     6     5     1     2
   13    14    15    16    13    14    15    19    17    14    15    16
   17    14    15    19    14    15    19    23    14    15    19    20
   16    15    19    23    16    15    19    20    15    19    23    21
   15    19    23    24    20    19    23    21    20    19    23    24
   19    23    21    17    19    23    21    22    24    23    21    17
   24    23    21    22    23    21    17    14    23    21    17    18
   22    21    17    14    22    21    17    18    21    17    14    15
   21    17    14    13    18    17    14    15    18    17    14    13



Thanks

Lin
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