[gmx-users] Problems with Dihedral transition times for dodecane

[ABEL Stephane 175950]

Daer all, 

I am trying to compute the transition times (TT) for all the CCCC angles in dodecane in the bulk (216) with gromacs 4.5.5

 I have constructed an index file with all CCCC angles (C1C2C3C4....C9C10C11C12) and for all the nine CCCC angles (C*C*C*C*) and use the following command for each angle. 

### C1C2C3C4

 g_angle_mpi -f 216_Dodecane_run_1.xtc -of 216_Dodecane_GRO54A7-Angle_9_Frac_Dihed.xvg -ot  216_Dodecane_GRO54A7_1_Trans_Dihed.xvg -ov 216_Dodecane_GRO54A7_1_Avg_Dihed.xvg -b 3000 -e 10000 -n 216_Dodecane_CCCC.ndx -type dihedral -noperiodic < Dih_1.txt

up to .

### C9C10C11C12 

 g_angle_mpi -f 216_Dodecane_run_1.xtc -of 216_Dodecane_GRO54A7-Angle_8_Frac_Dihed.xvg -ot  216_Dodecane_GRO54A7_8_Trans_Dihed.xvg -ov 216_Dodecane_GRO54A7_8_Avg_Dihed.xvg -b 3000 -e 10000 -n216_Dodecane_CCCC.ndx -type dihedral -noperiodic < Dih_8.txt

And for the last one for all CCCC angles

### CCCC 

g_angle_mpi -f 216_Dodecane_run_1.xtc -of 216_Dodecane_GRO54A7-Angle_9_Frac_Dihed.xvg -ot  216_Dodecane_GRO54A7_9_Trans_Dihed.xvg -ov 216_Dodecane_GRO54A7_9_Avg_Dihed.xvg -b 3000 -e 10000 -n 216_Dodecane_CCCC.ndx -type dihedral -noperiodic < Dih_9.txt

I obtain the following results for all the dihedral 

### C1C2C3C4

Now calculating transitions...
Total number of transitions:      28828
Time between transitions:        52.464 ps

### C2C3C4C5

Total number of transitions:      29821
Time between transitions:        50.717 ps

### C3C4C5C6

Now calculating transitions...
Total number of transitions:      33654
Time between transitions:        44.941 ps

### C4C5C6C7

Now calculating transitions...
Total number of transitions:      32206
Time between transitions:        46.961 ps

### C5C6C7C8

Now calculating transitions...
Total number of transitions:      31356
Time between transitions:        48.234 ps

### C6C7C8C9

Now calculating transitions...
Total number of transitions:      34014
Time between transitions:        44.465 ps

### C7C8C9C10

Total number of transitions:      31840
Time between transitions:        47.501 ps

### C8C9C10C11

Total number of transitions:      31885
Time between transitions:        47.434 ps

### C9C10C11C12C13

Total number of transitions:      30362
Time between transitions:        49.813 ps

And for all the CCCC angles in the dodecane 

Total number of transitions:      90546
Time between transitions:        50.110 ps
 
I am confused with these last values, where did they come from ? Why the Total number of transitions (90546): is not the sum of all the previous values. How these values are obtained. Note i have generated the index file for CCCC as following: aC* | aC* |  aC* | aC* 

Your advices are welcome. 

Stephane