GROMACS version: 2020
GROMACS modification: No
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I have been trying to run a protein bound nanosheet in gromacs. I follow the same protocol as given in the protein-ligand simuation. Initial minimization and equilibration, I perform in my local system and then for production simulation I use a supercomputer. The initial part runs well in my system but when I tried running the production in the supercomputer, I was getting Fatal error for domain decomposition. After trying several combinations, we concluded maybe we should remove the threading option and I used the minimum number of processors also.
Now I am getting this error:
Started mdrun on rank 0 Wed Jan 26 20:12:50 2022
Step Time 0 0.00000
Bond U-B Proper Dih. Improper Dih. CMAP Dih.
2.05481e+06 4.72149e+04 3.42955e+04 1.79522e+03 -1.09514e+03
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
1.23095e+04 1.32204e+05 9.33223e+05 -2.28270e+04 -4.92618e+06
Coul. recip. Potential Kinetic En. Total Energy Conserved En.
4.97211e+04 -1.68453e+06 6.61244e+05 -1.02328e+06 -1.02334e+06
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
3.06705e+02 -1.00951e+02 3.50016e+02 3.93654e-06
DD step 99 vol min/aver 1.000 load imb.: force 95.7% pme mesh/force 0.533
Program: mdrun_mpi_sp, version 2020.1
Source file: src/gromacs/domdec/cellsizes.cpp (line 651)
MPI rank: 0 (out of 64)
Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs
Surprisingly, if I try running this in local system it runs. Since, its my first time using a nanosheet in simulation, it would be very useful if someone can give me a feedback where I am going wrong or how to rectify the error and run the production simulation