2020-impi-mkl-PS2018-GOLD
I prepared all input file with amber force field via Charmm-GUI sever.
I am trying to apply minimization for DNA
gmx grompp -f step4.0_minimization.mdp -o step4.0_minimization.tpr -c step3_input.gro -r step3_input.gro -p topol.top -n index.ndx -maxwarn -1
The first command is working but the second one is giving an Fatal error
gmx d mdrun -v -deffnm step4.0_minimization
Fatal error:
There is no domain decomposition for 50 ranks that is compatible with the
given box and a minimum cell size of 1.5325 nm
Change the number of ranks or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
What I need to do?
A simple Google search will turn up lots of results about this error. It has been asked and answered many times. It is even an FAQ… Common errors when using GROMACS — GROMACS 2021.5 documentation
Unfortunately it does not work I tried.
gmx mdrun -v -deffnm em
Back Off! I just backed up em.log to ./#em.log.4#
Reading file em.tpr, VERSION 2020-UNCHECKED (single precision)
Program: gmx mdrun, version 2020-UNCHECKED
Source file: src/gromacs/domdec/domdec.cpp (line 2275)
MPI rank: 0 (out of 80)
Fatal error:
There is no domain decomposition for 60 ranks that is compatible with the
given box and a minimum cell size of 1.60751 nm
Change the number of ranks or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs
-rdd or -dds I have not found yet how they are working. Do have any advice?
Your system is too small to be split over so many cores. Use fewer.