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

gigo gigo at ibb.waw.pl
Fri Jul 4 12:00:08 CEST 2014

Dear Venkat and Teemu,
Thank you, that clarified the subject.


On 2014-07-04 06:57, Teemu Murtola wrote:
> 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:
>> Hi,
>> 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.

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