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

[David]

On Mon, 2005-07-25 at 09:59 -0400, Sukit Leekumjorn wrote:
> 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.
try tau_p = 20
> 
> 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
> 
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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