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. 

Appreciate, if anyone could help me.
Thank you.






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