[gmx-users] problem of running multiple cores

[Justin Lemkul]

On 3/15/14, 5:55 PM, Tom wrote:
> 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
> ./#dd_dump_err_0_n8.pdb.1#
>
> Back Off! I just backed up dd_dump_err_0_n21.pdb to
> ./#dd_dump_err_0_n21.pdb.1#
>
> Back Off! I just backed up dd_dump_err_0_n14.pdb to
> ./#dd_dump_err_0_n14.pdb.1#
>
> Back Off! I just backed up dd_dump_err_0_n5.pdb to
> ./#dd_dump_err_0_n5.pdb.1#
>
> Back Off! I just backed up dd_dump_err_0_n1.pdb to
> ./#dd_dump_err_0_n1.pdb.3#
> ...
> ---------------------------------------------------------------------------------
> I am wondering if it is because i did not assign charge group for this
> large surface.
>

Did you use "periodic_molecules = yes" in the .mdp file?

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================