Yes justin, the average is not 0 but around 0° (0.584577). But how to obtain the Average normalized CCCC dihedral distribution for example this dihedral? is few words the figure with g_angle ?
http://cmt.dur.ac.uk/sjc/thesis_dlc/node106.html Thank you again > sa wrote: > > 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 ? > > You're taking an average of the histogram of the angles, which I don't > think > actually corresponds to the true average. Your biggest peaks are at +/- > 180 > (i.e., trans dihedral), so I suspect your mean is likely not really 0. Use > g_angle -ov to get an actual average over time. > > -Justin > > > > > Thank you in advance for your advices > > > > SA > > > > > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > >
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