[gmx-users] fatal error:determinant in mdrun

[nanyu101]

Dear gmx-users,
  I have created a bigger lipid bilayer with genconf.
genconf -f popc128a.pdb -nbox 2 2 1 -dist 0 0 0 -o popc.pdb

And this bilayer is as big as four times of former bilayer.After doing that, I have run minimization for this big bilayer with cut-off for long distance electrostatic.
 title               =  Yo
cpp                 =  /lib/cpp
define              =  -DPOSRES
constraints         =  none
integrator          =  steep
emstep              =  0.001
emtol               =  10
nsteps              =  200000
nstcomm             =  1
nstxout             =  50
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
pbc                 =  xyz
ns_type             =  grid
coulombtype         =  cut-off
rlist               =  1.2
rcoulomb            =  1.8
rvdw                =  1.4
Tcoupl              =  no
Pcoupl              =  no                              
gen_vel             =  no
 

After minimizing my big bilayer,I tried to run NPT, but the system told me this:
Using Gromacs SSE single precision assembly innerloops.

           Step           Time         Lambda      Annealing
              0        0.00000        0.00000        1.00000

   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.004860  47622  47624   0.000779
        After LINCS         0.000078  19562  19563   0.000009

Fatal error: Determinant = 1325213994729268314112.000000


My operation mdp file and commands are listed as follows.
cpp                 =  /lib/cpp
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002	; ps !
nsteps              =  10000
nstcomm             =  1
comm_mode           =  angular
nstxout             =  50
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
pbc                 =  xyz
ns_type             =  grid
coulombtype         =  cut-off
fourierspacing      = 0.12
optimize_fft        = yes
rlist               =  1.0
rcoulomb            =  1.8
rvdw                =  1.4
Tcoupl              =  no
Pcoupl              =  berendsen
pcoupltype          =  anisotropic                              
tau_p               =  1   1   1   0   0   0
compressibility     =  4.5e-5  4.5e-5  4.5e-5  0.0  0.0  0.0
ref_p               =  1   1  1  0  0  0
gen_vel             =  yes
gen_temp            =  325.0
gen_seed            =  1
 

editconf -f popc.pdb -o popc.gro
editconf -bt cubic -f popc.gro -o popc.gro -c -center 0 0 0 -rotate 0 0 0
grompp -f md.mdp -c popc.gro -p popc.top -o popc.tpr
mdrun -v -deffmn popc


Any comments are recommended. Thanks a lot.

best wishes,
Xianhui Wu


 
______________________________________

===================================================================