[gmx-users] GMX 5.0.4 gmx gangle to choose the normal vector of a plane

[Mark Abraham]

On Wed, Apr 15, 2015 at 7:58 PM, LIANG Xujun <Xujun.LIANG at cea.fr> wrote:

> Dear Mark,
> >>Can't you get the angle you want by subtracting the one you have from 90?
> I've tried to solve by add 90, but I found that sometimes it's adding 90,
> sometimes it's subtracting, depending on the positions of the two planes?
>

There's only one angle between a vector and a plane (which was what you
originally asked about). By definition of the normal vector of a plane,
that angle is 90 minus the angle between that vector and the plane's
normal. So it seems like something is missing in your explanation (or my
understanding).

Mark

Xujun
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Mark
> Abraham [mark.j.abraham at gmail.com]
> Sent: Wednesday, April 15, 2015 18:23
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] GMX 5.0.4 gmx gangle to choose the normal vector
> of    a plane
>
> Hi,
>
> Can't you get the angle you want by subtracting the one you have from 90?
>
> Mark
> On 15/04/2015 5:58 pm, "LIANG Xujun" <Xujun.LIANG at cea.fr> wrote:
>
> > Dear GROMACS users,
> >
> > I am now using gromacs 5.0.4 to calculate the angle between the normal
> > vector of a plane 1 and the COM (center of mass) vector of plane 1 and
> > plane 2, I used the following command:
> >
> > gmx gangle -f *.xtc -s *.tpr -n *.ndx -g1 plane -group1 plane 1 (I tried
> > to use this command to select the normal vector of plane 1, but it
> doesn't
> > work!!) -g2 vector -group2 "com of group 1 plus com of group 2" (use this
> > to define the COM vector) -oav *.xvg
> >
> > But unfortunately, the results I obtained were the angle between plane 1
> > and COM vector, not normal vector of plane 1 with COM vector. Thus, couly
> > you please help me to define the plane normal vector in gromacs 5.0.4??
> >
> > Thanks very much in advance!
> >
> > Sincerely yours,
> > Xujun
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