[gmx-users] Re:6. QMMM, Segmentation fault (Olga Ivchenko)

[Olga Ivchenko]

Actually I am not sure that I can understand what is thread. But I can paste
QMMM file here:

title                    = my_mdp_file
cpp                      = /usr/bin/cpp -traditional
include                  =
define                   =


integrator               = md
tinit                    = 0
dt                       = 0.0005
nsteps                   = 2000
init_step                = 0
comm-mode                = Linear
nstcomm                  = 1
comm_grps                = system

emtol                    = 100.0
emstep                   = 0.0005

nstxout                  = 100
nstvout                  = 100
nstfout                  = 100
; Checkpointing helps you continue after crashes
nstcheckpoint            = 100
nstlog                   = 10
nstenergy                = 10
nstxtcout                = 10
;xtc-precision            = 1000
;xtc_grps                 = DNA

nstlist                  = 5
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.4
domain-decomposition     = no


coulombtype    = PME        ; Particle Mesh Ewald for long-range
electrostatics
pme_order    = 4        ; cubic interpolation
;fourierspacing    = 0.16        ; grid spacing for FFT


;coulombtype              = Cut-off
;rcoulomb-switch          = 0
rcoulomb                 = 1.4
epsilon_r                = 1
epsilon_rf               = 1

vdwtype                  = Cut-Off
rvdw-switch              = 0.
rvdw                     = 1.4
DispCorr                 = No

fourierspacing           = 0.12
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
;pme_order                = 4
ewald_rtol               = 1e-05
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = no

tcoupl                   = V-rescale
tc-grps                  = LIG SOL
tau-t                    = 0.1 0.1
ref-t                    = 309 309
Pcoupl                   = Berendsen
Pcoupltype               = Isotropic
tau-p                    = 1.0
compressibility          = 4.5e-5
ref-p                    = 1.0

QMMM                     = yes
QMMM-grps                = QMatoms
QMmethod                 = DFT
QMMMscheme               = ONIOM
QMbasis                  = sto-3g
QMcharge                 = 0
QMmult                   = 1

gen_vel                  = no
gen_temp                 = 00
gen_seed                 = 18111976

constraints              = all-bonds
constraint_algorithm     = LINCS
unconstrained_start      = no
Shake-SOR                = no
shake_tol                = 0.0001
lincs_order              = 4
lincs-iter               = 1
lincs_warnangle          = 30
morse                    = no

2010/12/7 Gerrit Groenhof <ggroenh at gwdg.de>

>
>
> Dera gromacs users,
>
> I am trying to do QMMM in the latest gromacs version :gromacs-4.5-beta2.
> When I run DFT I got an error:
>
> number of CPUs for gaussian = 1
> memory for gaussian = 50000000
> accuracy in l510 = 8
> NOT using cp-mcscf in l1003
> Level of SA at start = 0
> Segmentation fault
>
> Are you trying to use more than one thread?
>
> Gerrit
>
> Please could you advice me on this?
>
>  6. QMMM, Segmentation fault (Olga Ivchenko)
>>
>>
>>
> --
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