[gmx-users] Errors using GMX Density

ALEXANDER DHALIWAL dhaliak2 at mcmaster.ca
Wed Aug 10 23:13:25 CEST 2016

Dear GROMACS users,

I have been receiving errors when trying to calculate the electron
densities of different groups using gmx density. Here is an example of the
code used that generates these errors (ed_all_popccaff_extended.sh),
wherein I select my lipid bilayer group (POPC) to be the group centered
around and I select my solvent (SOL) to be the group whose electron density
I calculate:

gmx density -f md_150_cat.xtc -s md_150_cat.tpr -ei electrons_sol.dat -n
density_groups_popccaff.ndx -dens electron -b 100000 -e 150000 -o
edmap_150_cat_sol.xvg -center

The main errors I am receiving for this and similar commands have the
following forms:

*** Error in `gmx': double free or corruption (!prev): 0x0000000000d51b20
./ed_all_popccaff_extended.sh: line 33: 29187 Done 29188 Aborted
      (core dumped)

*** Error in `gmx': free(): invalid next size (fast): 0x000000000215d5b0 ***
./ed_all_popccaff_extended.sh: line 30: 29100 Done
     29101 Aborted                 (core dumped)

*** Error in `gmx': corrupted double-linked list: 0x0000000001441540 ***
Aborted (core dumped)

I was wondering if anyone had any experience rectifying these errors or
knew about whether or not this is a bug. The command works until the very
end before exiting with this error. Any help would be very appreciated.

Alex Dhaliwal
dhaliak2 at mcmaster.ca

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