[gmx-users] dynamic selection memory allocation problem

[gigo]

Dear GMXers,
I noticed, that the dynamic selection method, for example in gmx 
distance, easily fails because of the memory allocation problem.
I wanted to call gmx distance from a python script, which builds really 
long selections. An illustrating example, built of the same pairs of 
atoms connected by 'plus':

gmx distance -s eq03.tpr -f eq03.xtc -oall qweqwe.xvg -xvg none -select 
'((resid 14497 and resname SOL and name LP1) or (resname LIG and name 
P)) plus ((resid 14497 and resname SOL and name LP1) or (resname LIG and 
name P))'

This one works. However, if you add several '((resid 14497 and resname 
SOL and name LP1) or (resname LIG and name P))' blocks more (13 in this 
particular case), soon you will see something like:

*** Error in `gmx': realloc(): invalid next size: 0x0000000000fa57e0 ***
Abort

The rationale behind using the dynamic selection was simplification of 
the script that I've been working on - no need for writing and using an 
index file. I want to calculate about 40 different distances, which is 
currently far beyond the reach of gmx distance. I'm using 
gromacs-5.0-rc1. All limits related to memory allocation (stacksize etc) 
were removed. I tried it on a computer with loads of memory (and the 
number shown in the error message is rather small).
If you have any suggestions, I would be very grateful.
Best Regards,

Grzegorz Wieczorek