Hi all, I used the following line to obtain index file of RB dihedral quadrupltes:
mk_angndx -s *.tpr -n *-RB -type ryckaert-bellemans The resulting index file contains two groups [ RB-A1=1.88 ] [ RB-A1=-1.46 ] 1- Can anyone tell me please what these groups refer to? I am not able to find the answer in the manual. Then using g_angle -of option I compute dihedral fractions separately for each group. (figures attached) g_angle -f *.trr -n *-RB.ndx -of *_md-of-1.88 -b 2- The first peak of the first plot is not symmetrical as others although I collected data in the last 1 ns of a 20 ns simulation. does this mean the polymer chain has not equilibrated? this behavior is observed in the first few nanoseconds too. 3- I dont see why there are 3 peaks in the first group and 2 peaks in the [ RB-A1=-1.46 ] one? Appreciate greatly your help, Regards, On 1 March 2012 02:21, Mark Abraham <[email protected]> wrote: > On 1/03/2012 5:07 PM, Juliette N. wrote: > >> Hi all, >> >> Can anyone guide me how one can obtain dihedral distributions of a >> polymer chain and how this can be used to ensure the equilibration of >> system? >> g_angle takes a list of dihedrals and provides the dihedral distribution >> of a given dihedral in the time interval -b to -e ? >> > > Have a read of g_angle -h and try things out. You'll need to look in the > literature for info on the kind of information you're looking for. > > Mark > -- >
<<attachment: RB1.88.PNG>>
<<attachment: RB1.46.PNG>>
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