[gmx-users] Dihedral Angle Distribution

[Justin Lemkul]

On 4/16/18 3:07 AM, Anjana Jayasinghe wrote:
> Dear Gromacs Users,
> I want to calculate dihedral angle distribution for 9 dihedral angles in aliphatic chain of my molecule. I created the index file giving the command make_ndx -f run.gro -o dihedral.ndxThen  I typed,a C13 a C14 a C15 a C16a C14 a C15 a C16 a C17a C15 a C16 a C17 a C18a C16 a C17 a C18 a C19a C17 a C18 a C19 a C20a C18 a C19 a C20 a C21a C19 a C20 a C21 a C22a C20 a C21 a C22 a C23a C21 a C22 a C23 a C24
> When I checked the index file, all cerated groups contains more than four columns as below. I would like to know, is this correct or wrong? Since we need 4 atoms to represent the dihedral angle, [ C13_A_C14_A_C15_A_C16 ] group should contain 4 columns as highlighted below? I'm bit confused. Appreciate if anyone help me.
> [ C13_A_C14_A_C15_A_C16 ]
>    21   22   23   24   53   54   55   56   85   86   87   88  117  118  119
>   120  149  150  151  152  181  182  183  184  213  214  215  216  245  246
>   247  248  277  278  279  280  309  310  311  312  341  342  343  344  373
>   374  375  376  405  406  407  408  437  438  439  440  469  470  471  472
>   501  502  503  504  533  534  535  536  565  566  567  568  597  598  599
>   600  629  630  631  632  661  662  663  664  693  694  695  696  725  726
>   ........
> The other thing I want to know is, when I tried to calculate, angle distribution using the gromacs command,
> g_angle -f *.xtc -of Dihed.xvg -b 99000 -e 100000 -n dihedral.ndx -type dihedral, I got xvg file name as angdist.xvg instead of Dihed.xvg.

Because you didn't ask for a file named "Dihed.xvg" - the default output 
file name for the -od option is "angdist.xvg" so that's what g_angle wrote.

The index file is fine, when you specify dihedral mode, the program 
reads in groups of four numbers.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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