[gmx-users] Gromacs Orca QMMM segfault

[Groenhof, Gerrit]

INdeed, ORCA is not maintained at the moment. At least not by me, partially because it is not opensource (AFAIK).

The interface with gaussian is still working though. So my (poor) advice is either to keep using an older version of gromacs, or switch to gaussian, depending on the functionality you need most.

Best,

GErrit



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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