Dear GMXusers I would like to obtain the normalized CCCC dihedral distribution of the alkyl chain of DPC molecules simulated with the CHARMM ff and GMX4.5.3. So i used the g_angle tool. I have constructed an index file which contain the 9 corresponding angles with make_index_mpi:
a C12 | a C13 | a C14 | a C15 ---> consecutive atoms ... a C20 | a C21 | a C22 | aC23 and used g_angle command g_angle_mpi -f *.xtc -ov DPC-Self-CHA_100-155ns-Angle_0_Dihed.xvg -b 100000 -e 110000 -n Tail_dihedral_index.ndx -type dihedral For example by choosing the C15_C16_C17_C18 dihedral angle located in the middle of the alkyl chain, i obtain an average value 0° (!!) and the following figure http://www.hostingpics.net/viewer.php?id=825755angdist.png This is not what i expect How to obtain simply the classical normalized function from g_angle ? Thank you in advance for your advices SA
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