[gmx-users] problem of running multiple cores

Tom dnaafm at gmail.com
Sat Mar 15 22:55:16 CET 2014

Dear Gromacs Users

I created a Silca surface with PBC bonding with the image atoms and assigned
all the intramolecular potentials.

It is strange that the generated *tpr can not be run with Multiple cores.
It Only works
well on single core.

This is the warning when I grompp:
WARNING 1 [file grompp.mdp]:
  The sum of the two largest charge group radii (16.834835) is larger than
  rlist (1.200000)

This is the error message if i run mdrun using more than 1 core:
WARNING: Listed nonbonded interaction between particles 8512 and 8550
at distance 3f which is larger than the table limit 3f nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

A list of missing interactions:
                Bond of  13260 missing    385
                 U-B of  25500 missing   1322
               LJ-14 of  37332 missing   1685

Molecule type 'ICE'
the first 10 missing interactions, except for exclusions:
                Bond atoms    110387           global     1 10387
                 U-B atoms    1  58810382      global     1   588 10382
                 U-B atoms    110387  575      global     1 10387   575
               LJ-14 atoms    1  593           global     1   593
               LJ-14 atoms    1  596           global     1   596
               LJ-14 atoms    1  598           global     1   598
               LJ-14 atoms    110385           global     1 10385
                 U-B atoms    2  589 1185      global     2   589  1185
                 U-B atoms    2 1209  576      global     2  1209   576
               LJ-14 atoms    2  599           global     2   599

Back Off! I just backed up dd_dump_err_0_n8.pdb to

Back Off! I just backed up dd_dump_err_0_n21.pdb to

Back Off! I just backed up dd_dump_err_0_n14.pdb to

Back Off! I just backed up dd_dump_err_0_n5.pdb to

Back Off! I just backed up dd_dump_err_0_n1.pdb to
I am wondering if it is because i did not assign charge group for this
large surface.

Thanks a lot for your suggestions!


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