[gmx-users] g_angle output

David van der Spoel spoel at xray.bmc.uu.se
Fri May 20 13:01:07 CEST 2005

On Fri, 2005-05-20 at 12:41 +0200, UCT Staff Member - Jackson wrote:
> I have a cyclic peptide which when I start a high temperature dynamic
> run has all peptide bonds trans.  After cluster analysis of the
> trajectors I find the lowest energy conformation to have two cis peptide
> bonds.  I am now trying to monitor the peptide dihedral angles during
> the run to see when  this trans/cis isomerisation occurs. 
> I have used:
> g_angle -f xx.trr -s xx.tpr -n xx.ndx -all
> I am then prompted to select an angle from the index list. I have to
> repeat this for every angle in the list.
> I have 2 questions:
> How do I get g_angle to do the whole list automatically?
By putting all dihedrals in one index group
(remember the -type dihedral)

> What does the output mean?  Accoding to the manual it should have the
> average and the individual angles.  However if I look at the file for
> one of the angles it has 3 columns, the time and 2 angles.  The first
> angle does not look like the average.
Don't know...
> Thanks
> Graham
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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