Open makson96 opened 6 years ago
Using mdrum with "-ntmpi 1" results in:
...
GROMACS: gmx mdrun, version 2018
Executable: /home/makson/Publiczny/Dynamics/gromacs/gromacs-2018/install/bin//gmx
Data prefix: /home/makson/Publiczny/Dynamics/gromacs/gromacs-2018/install
Working dir: /home/makson/.dynamics/cpeptide_test/test
Command line:
gmx mdrun -nice 4 -s cpeptide_em -o cpeptide_em -c cpeptide_b4pr -v -ntmpi 1
Back Off! I just backed up md.log to ./#md.log.1#
Reading file cpeptide_em.tpr, VERSION 2018 (single precision)
No option -multi
Using 1 MPI thread
NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
removed in a future release when 'verlet' supports all interaction forms.
Back Off! I just backed up cpeptide_em.trr to ./#cpeptide_em.trr.1#
Back Off! I just backed up ener.edr to ./#ener.edr.1#
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 10000
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Program: gmx mdrun, version 2018
Source file: src/gromacs/gmxlib/nonbonded/nb_generic.cpp (line 298)
Fatal error:
Death & horror! GB generic interaction not implemented.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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If I use "ns_type = grid" instead of simple I got:
...
GROMACS: gmx mdrun, version 2018
Executable: /home/makson/Publiczny/Dynamics/gromacs/gromacs-2018/install/bin//gmx
Data prefix: /home/makson/Publiczny/Dynamics/gromacs/gromacs-2018/install
Working dir: /home/makson/.dynamics/cpeptide_test/test
Command line:
gmx mdrun -nice 4 -s cpeptide_em -o cpeptide_em -c cpeptide_b4pr -v
Back Off! I just backed up md.log to ./#md.log.2#
Reading file cpeptide_em.tpr, VERSION 2018 (single precision)
NOTE: Parallelization is limited by the small number of atoms,
only starting 2 thread-MPI ranks.
You can use the -nt and/or -ntmpi option to optimize the number of threads.
NOTE: disabling dynamic load balancing as it is only supported with dynamics, not with integrator 'steep'.
and GROMACS hangs. I can not use 'Verlet' cutoff-scheme instead of 'group', because verlet does not support implicit solvent yet.
I hope that GROMACS 2018 point releases will address this issue. For now it needs to stay open.
When using simple implicit solvent simulation on default options with GROMACS 2018, the fallowing error message is generated during gmx mdrum:
the mdp file is: