[gmx-users] command line with gmx_mpi gangle for choosing the vector formed by coms of two planes

Mark Abraham mark.j.abraham at gmail.com
Wed Apr 8 10:46:44 CEST 2015

On Wed, Apr 8, 2015 at 10:33 AM, LIANG Xujun <Xujun.LIANG at cea.fr> wrote:

> Hello all,
> I have one question:
> I would like to compute the angle between the normal vector of plane 1 and
> the com vector of plane 1 and plane 2 using gmx_mpi gangle (version 5.0.4).
> The command is as follows:
> gmx_mpi gangle -f ....xtc -s ....tpr -n ....ndx -g1 plane -group1 -g2
> vector -group2 -oav test_angle_vector.xvg -b .. -e ...
> After enter the above command, I need to make the following choices:
> 0- <enter>-<ctrl-D>-com of group 0 plus com of group 1-<enter>-<ctrl-D>
> For automatically analyzing, I wrote the above choice into a text
> file----echo -e "0\r com of group 0 plus com of group 1\r",  unfortunately,
> it doesn't work.

Probably \r is not sufficient, follow
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts. But
I understand that it t is intended that you pass selection strings directly
to -group1 and -group2 (see gmx gangle -h) so doing that might work better.


> Could you please tell me how can I achieve the above goal?
> Thanks for your help in advance!
> Xujun
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