[gmx-users] Gromacs Orca QMMM segfault

[Mark Abraham]

Hi,

Yes that's pretty likely, given the lack of maintenance on this feature.

Mark

On Thu, 23 Jun 2016 23:40 Thilo Mast <thilo.mast at kit.edu> wrote:

> Okay, I've found the problem.
> I think there is a problem between the communication of Gromacs v5.x and
> ORCA.
> When I use Gromacs v4.6.7 it works ...
>
>
> Am 23.06.2016 um 15:29 schrieb Thilo Mast:
> > Hi GMX users,
> >
> > I'm trying to run a QM/MM simulation with Gromacs v5.0 and ORCA v3.0.1.
> > The energy minimization of my system works! However, when I try to
> > start the MD simulation with mdrun_d -nt 1 -deffnm nvt I get the
> > following error:
> >
> > Layer 0
> > nr of QM atoms 51
> > QMlevel: RHF/3-21G*
> >
> > Setting ORCA path to: /usr/local/run/orca-3.0.1...
> > ORCA initialised...
> >
> > 10000 steps,      5.0 ps.
> > Segmentation fault
> >
> > I've set the environment variables $GMX_QM_ORCA_BASENAME to "nvt" and
> > $GMX_ORCA_PATH to the path where the ORCA executable is located.
> >
> > My nvt.ORCAINFO has the following structure:
> > ! B3LYP D3BJ def2-SVP
> >
> > %method
> >  Grid        2
> >  FinalGrid   4
> > end
> >
> > My nvt.mdp has the following structure:
> > integrator      = md
> > nsteps          = 10000
> > dt              = 0.0005
> > ; Output control
> > nstxout         = 100
> > nstvout         = 100
> > nstxout-compressed = 0
> > nstenergy       = 100
> > nstlog          = 100
> > ; Bond parameters
> > continuation            = no
> > constraint_algorithm    = lincs
> > constraints             = h-bonds
> > ; Neighborsearching
> > cutoff-scheme       = group
> > ns_type             = grid
> > nstlist             = 10
> > rlist            = 1.2
> > rcoulomb            = 1.2
> > rvdw                = 1.2
> > ; Electrostatics
> > coulombtype         = PME
> > ; Temperature coupling is on
> > tcoupl          = V-rescale
> > nsttcouple    = 1
> > tc-grps         = System
> > tau_t           = 0.1
> > ref_t           = 300
> > ; Pressure coupling is off
> > pcoupl          = no
> > ; Periodic boundary conditions
> > pbc             = xyz
> > ; Dispersion correction
> > DispCorr        = no
> > ; Velocity generation
> > gen_vel         = yes
> > gen_temp        = 300
> > gen_seed        = -1
> > ; OPTIONS FOR QMMM calculations
> > QMMM                     = yes
> > QMMM-grps                = QM
> > QMmethod                 = RHF        ; is ignored
> > QMMMscheme               = normal
> > QMbasis                  = 3-21G*    ; is ignored
> > QMcharge                 = -1
> > QMmult                   = 1
> >
> > Can anyone please help me?
> >
> > Best
> > Thilo
> >
>
> --
>
>
>       M. Sc. Thilo Mast
>       Karlsruhe Institute of Technology (KIT)
>       Institute of Physical Chemistry - Theoretical Chemical Biology
>       Building 30.25
>       Kaiserstr. 12
>       76131 Karlsruhe
>
>       Mail: thilo.mast at kit.edu <mailto:thilo.mast at kit.edu>
>       Phone: +49 (0) 721 / 608-43572
>
> --
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