grompp running out of memory when excluded bonded neighbours is large - Redmine #2260
Archive from user: Dallas Warren
Want to be able to exclude intramolecular contributions to RDFs for long linear molecules (38 united atoms long). When run grompp to exclude all atoms (nrexcl=37) within a molecule, memory gets used up and grompp is killed.
System comprises of 60 linear molecules containing 38 united atoms, with water and couple of toluene. Total atoms 64,875
Command using: gmx grompp -f md -c md_0 -t md_0 -p topol -o md_1
Attached tar includes .mdp .itp .top .gro .trr and ff files to enable generation of the tpr
C12E8.itp file currently has exclusion set to 37, which it runs out of memory with (36GB available).
My question to the emailing list about this: https://mailman-1.sys.kth.se/pipermail/gromacs.org\_gmx-users/2017-September/116102.html
(from redmine: issue id 2260, created on 2017-10-04 by gmxdefault, closed on 2018-01-03)
- Revision b7d5d939 by Erik Lindahl on 2018-01-03T13:02:25Z:
Fix complexity for large exclusion orders To avoid exploding computational complexity for highly connected molecules with large values for excluded neighbors, avoid adding a neighbor to the temporary nnb structure if it is already present as a lower-order neighbor. Fixes #2260. Change-Id: I30c27a281ddcbbac175f79ab9d5bba49f2f988ae
- exclusions_large.tar.gz Required files to run grompp with