[gmx-users] "Segmentation fault" in mdrun

[Monique Brito]

Hi gromacs people!

It has occuring an error in my simulation in
vacuo. It appears as "segmentation fault"
before completing the mdrun.
In the archive md.log it has a LINCS WARNING and
the following phrase: "Constraint error in
algorithm Lincs at step -1". But I'm not using
constraint, as you could see below.

The em and md.mdp I'm using are as follows.


em.mdp

cpp                 =  /lib/cpp
define              =  -DPOSRES -DFLEX_SPC
constraints         =  none
integrator          =  steep
nsteps              =  10000
;
;       Energy minimizing stuff
;
emtol               =  100
emstep              =  0.00001

nstcomm             =  1
ns_type             =  grid
rlist               =  1.5
rcoulomb            =  1.5
rvdw                =  1.5
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no


md.mdp


define                   = -DFLEX_SPC
constraints              = none
integrator               = md
dt                       = 0.002
tinit                    = 0
nsteps                   = 25000 ; 50 ps
simulation
comm_mode                = linear
nstcomm                  = 1
comm_grps                = Protein  MKC


nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 1
rcoulomb_switch          = 0
rcoulomb                 = 0.9
epsilon_r                = 1
vdwtype                  = Switch
rvdw_switch              = 0
rvdw                     = 0.9


coulombtype              = Switch
pme_order                = 6
optimize_fft             = yes


tcoupl                   = Berendsen
tc-grps                  = Protein  MKC
tau_t                    = 0.1      0.1
ref_t                    = 300      300


nstxout                  = 500
nstvout                  = 0
nstlog                   = 10
nstenergy                = 10
nstxtcout                = 0
energygrps               = Protein  MKC


gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 173529

Any help?
Cheers,
Monique Brito.

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