Bonded interaction error when extending a simulation

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1

GROMACS version: 2021.1
GROMACS modification: No

Hi,

I’ve run simulations for multiple systems for 200ns, but when I tried to extend the simulation to 500ns, I got a bonded interaction error. The same thing happened to a system in the middle of a 3µs simulation run. I’m using the CHARMM C36M forcefield for all the simulations. I thought my system might not have been well minimized, but it didn’t blow up for 200ns and over 1µs and the potential energy converged during minimization. I’m running everything in a single node of a cluster, with four V100 nvidia GPUs and 48 CPU cores without MPI. I’ve run systems of the same size on the same node configuration without any issue.

The command I used to extend the simulation was:

gmx convert-tpr -s md.tpr -until 500000 -o md.tpr

gmx mdrun -deffnm md -cpi md.cpt -append

The error message I got was:

 gmx mdrun -deffnm md -cpi md.cpt -append

Compiled SIMD: AVX_256, but for this host/run AVX_512 might be better (see
log).
Reading file md.tpr, VERSION 2021.1 (single precision)
Changing nstlist from 25 to 100, rlist from 1.239 to 1.345

On host sdumont8052 4 GPUs selected for this run.
Mapping of GPU IDs to the 8 GPU tasks in the 8 ranks on this node:
  PP:0,PP:0,PP:1,PP:1,PP:2,PP:2,PP:3,PP:3
PP tasks will do (non-perturbed) short-ranged and most bonded interactions on the GPU
PP task will update and constrain coordinates on the CPU
Using 8 MPI threads
Using 6 OpenMP threads per tMPI thread


NOTE: DLB will not turn on during the first phase of PME tuning

Not all bonded interactions have been properly assigned to the domain decomposition cells
A list of missing interactions:
                Bond of   2600 missing     26
                 U-B of   8884 missing    134
         Proper Dih. of  12671 missing    325
       Improper Dih. of    810 missing      4
           CMAP Dih. of    310 missing      3
               LJ-14 of  12790 missing    180
Molecule type 'Protein'
the first 10 missing interactions, except for exclusions:
         Proper Dih. atoms 1063 1078 1080 1084 global  1063  1078  1080  1084
         Proper Dih. atoms 1063 1078 1080 1084 global  1063  1078  1080  1084
               LJ-14 atoms 1063 1084           global  1063  1084
                 U-B atoms 1078 1080 1084      global  1078  1080  1084
         Proper Dih. atoms 1078 1080 1084 1085 global  1078  1080  1084  1085
         Proper Dih. atoms 1078 1080 1084 1086 global  1078  1080  1084  1086
         Proper Dih. atoms 1078 1080 1084 1092 global  1078  1080  1084  1092
           CMAP Dih. atoms 1078 1080 1084 1092 1094 global  1078  1080  1084  1092  1094
               LJ-14 atoms 1078 1085           global  1078  1085
         Proper Dih. atoms 1079 1078 1080 1084 global  1079  1078  1080  1084




-------------------------------------------------------
Program:     gmx mdrun, version 2021.1
Source file: src/gromacs/domdec/domdec_topology.cpp (line 453)
MPI rank:    0 (out of 8)

Fatal error:
672 of the 55678 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(0.766616 nm) or the two-body cut-off distance (1.62275 nm), see option -rdd,
for pairs and tabulated bonds also see option -ddcheck

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I have absolutely no clue about what is going on.

Any help will be appreciated

Thanks