[gmx-users] dynamic selection memory allocation problem

gigo gigo at ibb.waw.pl
Fri Jun 27 15:28:20 CEST 2014

Dear Teemu,
Thank you for your reply.

> Please file a report a <http://redmine.gromacs.org> with files and the
> exact selection necessary to reproduce the problem (a single .gro 
> structure
> is likely sufficient).

I will do so.

> While your approach is likely a very inefficient way
> to use the selections (plus/merge is not designed for massive copying, 
> and
> your selection probably evaluates some parts multiple times over all 
> the
> atoms in the system), it would be useful to find out what is the actual
> problem.

OK. What approach would you suggest for calculating many distances 
without writing an index file then?

> Your example is not particularly illustrative, as there is no point in
> computing the same distance 15 times...

The purpose of the example was to show that the dynamic selection 
mechanism has a limited capacity in terms of the length of the input 
string, and not to show that my research is of any value for anybody. Id 
did the job, so it was illustrative.

Thank you once more,


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