[gmx-users] how to use g_angle to get the average dihedral angle ?

[maggin]

Hi,

I use g_angle and want to get the average dihedral angle, so operation as
follow:

(1) mk_angndx -s md_0_1.tpr -n angle.ndx  -type  dihedral

and get angle.ndx :

[ Phi=180.0_2_43.93 ]
     4    17    15    16     9    13    12    14    19    33    31    32
    35    49    47    48    50    63    61    62    65    80    78    79
    82   102   100   101   104   124   122   123   126   141   139   140
   143   158   156   157   160   180   178   179   182   192   190   191
   184   188   187   189   194   212   210   211   214   231   229   230
   233   246   244   245   238   242   241   243   248   268   266   267
   270   287   285   286   289   294   292   293   296   301   299   300
   303   319   318   320
[ Phi=180.0_2_4.18 ]
    15    19    17    18    31    35    33    34    47    50    49    58
    61    65    63    64    74    72    76    77    78    82    80    81
   100   104   102   103   122   126   124   125   139   143   141   142
   152   150   154   155   156   160   158   159   178   182   180   181
   190   194   192   193   210   214   212   213   229   233   231   232
   244   248   246   247   266   270   268   269   285   289   287   288
   292   296   294   295   299   303   301   302
[ Phi=180.0_2_4.60 ]
    67    70    72    71    70    76    72    73    71    76    74    75
   145   148   150   149   148   154   150   151   149   154   152   153
   196   199   202   200   199   204   200   201   199   206   202   203
   200   208   204   205   202   208   206   207   204   206   208   209

(2)  g_angle  -n angle.ndx -type dihedral -ov  -all 

and get:
Group     0 (Phi=180.0_2_43.93) has    88 elements
Group     1 (Phi=180.0_2_4.18) has    80 elements
Group     2 (Phi=180.0_2_4.60) has    48 elements
Select a group:

At this step, I want to get the average dihedral angle of a peptide, but it
appear Group 0, Group 1, Group 2. So, how to get average dihedral angle as a
whole , not seperate in groups?

Thank you very much!

maggin

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