[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.
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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