[gmx-users] Dihedral angles distribution

sa sagmx.mail at gmail.com
Mon Mar 7 12:52:10 CET 2011

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


This  is not what i expect How to obtain simply the classical normalized
function from g_angle ?

Thank you in advance for your advices

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