makson96 / Dynamics

Dynamics PyMOL Plugin
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Default implicit solvent fails with GROMACS 2018 #96

Open makson96 opened 6 years ago

makson96 commented 6 years ago

When using simple implicit solvent simulation on default options with GROMACS 2018, the fallowing error message is generated during gmx mdrum:

Fatal error:
Domain decomposition does not support simple neighbor searching, use grid
searching or run with one MPI rank

the mdp file is:

define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 10000
nstlist = 10
ns_type = simple
rlist = 0
rcoulomb = 0
rvdw = 0
emtol = 1000.0
emstep = 0.01
implicit-solvent = GBSA
gb-algorithm = Still
pbc = no
rgbradii = 0
cutoff-scheme = group
coulombtype = Cut-off
makson96 commented 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

-------------------------------------------------------
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
-------------------------------------------------------

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.