[gmx-users] problem with calculating angles and dynamic selections
teemu.murtola at gmail.com
Fri Jul 4 06:57:49 CEST 2014
No, this is not a bug, but a result of a conscious design. Internally, the
selections are always evaluated as sets of atoms, which are (currently)
handled as a sorted list of indices. So any basic selection operation
always results in sorted atoms. If you want something else, you can use
"permute", "merge" or "plus" (which is only necessary for those few tools
that put significance to the order of atoms).
In addition to simplifying the implementation, this is much clearer. Or
what order would you expect the atoms to be if you provide a selection
"name C A B", and your system has 10 A atoms, 5 B atoms and 3 C atoms? How
about if the system has molecules with multiple residues (so that splitting
by molecule or by residue results in different ordering)? Or if you combine
two arbitrary unsorted expressions with "and" or "or"?
On Jul 3, 2014 8:04 PM, "Venkat Reddy" <venkat4bt at gmail.com> wrote:
> 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
> > 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
> > 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
> > 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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