# [gmx-users] dihedral distributions

Juliette N. joojoojooon at gmail.com
Fri Mar 2 02:42:06 CET 2012

```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?

Regards,

On 1 March 2012 02:21, Mark Abraham <Mark.Abraham at anu.edu.au> 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
> --
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120301/e812dbaf/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RB1.88.PNG
Type: image/png
Size: 9359 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120301/e812dbaf/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RB1.46.PNG
Type: image/png
Size: 9580 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120301/e812dbaf/attachment-0001.png>
```