[gmx-users] WARNING: your box is exploding!

[Sukit Leekumjorn]

Hello Gmx-Users

I am running PME from Gromacs3.3 beta version.  I was able  to run lipid 
bilayer system (single bilayer for more than 20ns) with PME however when 
I double the bilayer in the z direction using genconf (1 1 2) and using 
the same .mdp and .top, the warning below started to appear. I try 
changing several input in the mdp file such as (reducing time step: 
1-2fs, pme: 8-10 order, Fourier spacing: 0.1-0.12 , pcoupling type: 
isotropic-anisotropic and changing velocity random seed), nothing work. 
Then I tried equilibrate the structure using twin cut-off (work fine) 
and then switch to PME (warning everywhere).  I suspected it was the 
total pressure of the system because it start off with over 1000 bar. It 
should not be that high because I used the structure from previous PME 
equilibration which did not give any error. If anyone encounter similar 
situation, please let me know how to overcome this problem. I also 
include my mdp file below.

Thank in advance
Sukit

Grid: 24 x 22 x 43 cells
WARNING: your box is exploding! (ncells = 22704)
           Step           Time         Lambda
          58000      116.00001        0.00000

   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.004526   1465   1466   0.001213
        After LINCS         0.000033    115    116   0.000005

   Energies (kJ/mol)
          Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.          LJ-14
    5.65804e+04    1.60176e+04    3.02897e+04    1.86966e+03    1.69267e+04
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
    3.79467e+04    1.22259e+04    1.41573e+04   -7.54301e+05   -5.85245e+05
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
   -1.15353e+06    1.92881e+05   -9.60651e+05    3.22489e+02    1.95346e+02

title                    = pure bilayer
cpp                      = /usr/bin/cpp
include                  = -I../ffsukit
define                   =
integrator               = md
dt                       = 0.002
nsteps                   = 1000000
nstxout                  = 1000
nstvout                  = 1000
nstlog                   = 1000
nstenergy                = 1000
nstxtcout                =
xtc_grps                 =
energygrps               =
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 0.9
coulombtype              = PME
rcoulomb                 = 0.9
rvdw                     = 0.9
vdw-type                 = Cut-off
DispCorr                 = EnerPres
fourierspacing           = 0.1
pme_order                = 10
ewald_rtol               = 1e-05
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = yes
tcoupl                   = Berendsen
tc_grps                  = DPPC WAT
tau_t                    = 0.1 0.1
ref_t                    = 323 323
Pcoupl                   = Berendsen
Pcoupltype               = anisotropic
tau_p                    = 2.0
compressibility          = 4.6e-5 4.6e-5 4.6e-5 0.0 0.0 0.0
ref_p                    = 1.0 1.0 1.0 0.0 0.0 0.0
gen_vel                  = yes
gen_temp                 = 323
gen_seed                 = 12345
constraints              = all-bonds
constraint-algorithm     = Lincs
unconstrained-start      = no
lincs-order              = 4