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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
