OK, i will try your suggestion. Thank you
SA sa wrote: > > 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 > > > > The output you will get from Gromacs will have all angles within the range > of > {-180..180}, not {0..360}, as shown in that plot. I think this simply > derives > from a difference in convention. You would have to post-process the data > to > shift the angles to correspond to the display range you want. Gromacs does > not > do this for you. To get the "correct" average angle, use g_angle > -noperiodic. > > -Justin > > > 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 <http://vt.edu> | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > ======================================== > > > > > > -- > >
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