[gmx-users] dynamic selection memory allocation problem

Teemu Murtola teemu.murtola at gmail.com
Fri Jun 27 15:48:40 CEST 2014

My point about being non-illustrative was that it is impossible for people
to suggest alternative solutions if they don't know what you are trying to
achieve. If you really want to calculate the same distance multiple times,
I'd suggest to calculate it just once, and have a postprocessing script to
duplicate it in the output.
On Jun 27, 2014 4:28 PM, "gigo" <gigo at ibb.waw.pl> wrote:

> 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,
> g
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