[gmx-users] Regarding gmx gangle selection

[Venkat Reddy]

Thank you Sir for the clarification.


On Wed, Jul 9, 2014 at 3:57 PM, Teemu Murtola <teemu.murtola at gmail.com>
wrote:

> The vector is from the first position to the second, from the third to the
> fourth and so on. But the order of parameters for, e.g., "name", does not
> affect the order of positions (see earlier discussion on the list): the
> atoms are always selected in the order of increasing atom indices. If you
> want to reverse the vector, you can use "permute 2 1" at the end of the
> selection.
> On Jul 9, 2014 10:03 AM, "Venkat Reddy" <venkat4bt at gmail.com> wrote:
>
> > Hi,
> > Apologies for the minor mistake in typing. Actually the argument in
> group1
> > should be 'Resname RES and name B A'. Sorry for the confusion.
> >
> >
> > On Wed, Jul 9, 2014 at 12:19 PM, Venkat Reddy <venkat4bt at gmail.com>
> wrote:
> >
> > > Dear all,
> > > I am trying to analyse my lipid vesicle system using gromacs-5.0. I am
> > > using gmx gangle to find the angle between lipid tails. In the gmx
> gangle
> > > help section, its mentioned that "For vectors, the selected positions
> set
> > > the endpoints of the vector". But nothing is mentioned about direction
> of
> > > vector. For example, if I select  'Resname RES and name A B' to denote
> my
> > > vector; The direction of the vector is from A to B. Please correct me
> if
> > I
> > > am wrong.
> > >
> > > If I want to calculate the angle ABC in a residue RES, -group1 'Resname
> > > RES and name A B' -group2 'Resname RES and name B C', is this a valid
> > > selection?
> > >
> > > --
> > > With Best Wishes
> > > Venkat Reddy Chirasani
> > > PhD student
> > > Laboratory of Computational Biophysics
> > > Department of Biotechnology
> > > IIT Madras
> > > Chennai
> > > INDIA-600036
> > >
> >
> >
> >
> > --
> > With Best Wishes
> > Venkat Reddy Chirasani
> > PhD student
> > Laboratory of Computational Biophysics
> > Department of Biotechnology
> > IIT Madras
> > Chennai
> > INDIA-600036
> > --
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036