[gmx-users] Regarding g_sgangle index file

Teemu Murtola teemu.murtola at gmail.com
Tue Sep 24 20:59:18 CEST 2013


On Tue, Sep 24, 2013 at 8:39 AM, Venkat Reddy <venkat4bt at gmail.com> wrote:

> I have been using the new tool "gmx gangle". My actual intention is to
> calculate the orientation between any two same molecules (say cholesterol)
> throughout the trajectory and there are 40 cholesterol molecules. But I
> couldn't calculate it. I am getting "0" as output. My command is:
> gmx gangle -f traj_noPBC.xtc -s topol.tpr -n -g1 vector -g2 vector -group1
> 'resname CHOL and name R5 R0' -group2 'resname CHOL and name R5 R0' -oav
> -oall -oh

In its present form, the tool cannot (easily) do what you want. It only
supports calculating either a single angle, or a set of angles between
fixed pairs of vectors. In your case, you are requesting the tool to
calculate the R5-R0 angle between molecules 1-1, 2-2, and so on. Since for
all angles, the input vectors are identical, a zero angle is the expected

It should not be too difficult to extend the tool to do at least part of
what you want, by adding an option to either calculate angles from one
vector to a set of vectors (e.g., "resname CHOL and resnr N and name R5 R0'
and 'resname CHOL and name R5 R0'), or even to calculate the angles between
all pairs of vectors.

If you have programming experience and would like to extend the tool, feel
free to submit your change to gerrit.gromacs.org; I'm more than happy to
review and provide comments.

Best regards,

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