Hi all,<br><br>I used the following line to obtain index file of RB dihedral quadrupltes:<br><br>mk_angndx -s *.tpr -n *-RB -type ryckaert-bellemans<br><br>The resulting index file contains two groups<br><br>[ RB-A1=1.88 ]<br>
<br>[ RB-A1=-1.46 ]<br><br>1- Can anyone tell me please what these groups refer to? I am not able to find the answer in the manual. <br><br>Then using g_angle -of option I compute dihedral fractions separately for each group. (figures attached)<br>
<br>g_angle -f *.trr -n *-RB.ndx -of *_md-of-1.88 -b <br><br>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. <br>
<br>3- I dont see why there are 3 peaks in the first group and 2 peaks in the [ RB-A1=-1.46 ] one? <br><br><br>Appreciate greatly your help, <br>Regards,<br><br><br><div class="gmail_quote">On 1 March 2012 02:21, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div></div><div class="h5">On 1/03/2012 5:07 PM, Juliette N. wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<br>
<br>
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?<br>
g_angle takes a list of dihedrals and provides the dihedral distribution of a given dihedral in the time interval -b to -e ?<br>
</blockquote>
<br></div></div>
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.<br>
<br>
Mark<br><font color="#888888">
-- </font><br></blockquote></div><br>