[gmx-users] Problems with Dihedral transition times for dodecane
ABEL Stephane 175950
Stephane.ABEL at cea.fr
Thu Jun 28 15:51:23 CEST 2012
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
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