[gmx-users] problem with calculating angles and dynamic selections

Venkat Reddy venkat4bt at gmail.com
Thu Jul 3 20:04:13 CEST 2014

I have tried gmx gangle -g1 angle option. Its sorting the atoms specified
in the input. I think it might be a bug. gmx gangle  -g1 vector -g2 vector
is doing fine.

On Thu, Jul 3, 2014 at 7:42 PM, gigo <gigo at ibb.waw.pl> wrote:

> Hi!
> I find it impossible to calculate (some) angles between atoms using
> dynamic selection in 'gmx gangle' command. The problem is, that the dynamic
> selection mechanism persistently sorts numbers of atoms specified in the
> input. So, if I have atoms A, B and C with ascending indexes, I am not able
> to calculate angle B-A-C - I only get value for A-B-C, no matter how I
> order them in the command line. Is there any way to do it without writing
> an index file (which I have to parse anyway, because the same mechanism
> sorts atoms in 'gmx select'...)? If not, I will submit a feature request on
> redmine - something like -nosort option...
> Regards,
> Grzegorz Wieczorek
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With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras

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