[gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3

Chih-Ying Lin chihying2008 at gmail.com
Fri Jan 1 23:35:01 CET 2010


 Hi
I used Gromacs version 3.3.3.
My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7
)
MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64   => 16 nodes in total
After doing the energy minimization, => the potential energy is extremely
high ( say, ten to the 9th order )
I visualized the " Simulation-System-EM-solvated.gro " after the energy
minimization.
Then, I found that the Simulation Sysmtem is devided into 16 domains very
clearly and the molecules (protein, ligand, and water) break into atoms in
the boundaries.
I have checked that the 20 ligands are not overlapped each other and are not
overlapped with protein from the beginning.

More, i have created 10 alike system and each is with "one protein + 20
ligand + water molecules"
Two of them get the "minus potential energy" after energy minimization and I
can continue running the MD simulation successfully.
Others of them get the "extreme high positive potential energy" and the
system is devided into 16 domains after energy minimization and the
simulation broke afterall.

With one protein + 10 ligand + water molecules, ( 6 x 6 x 6 )
There is no problems like that.
Please give me your ideas to solve the problem.
The commands are listed below and the .tpr file created by grompp is
attached.

Thank you
Lin



1. pdb2gmx_mpi -f 6LYZ.pdb -o 6LYZ.gro -p 6LYZ.top      => G 45a3
2. Energy minimization of the structure (vacuum)
 pbc = no,
grompp_mpi -np 16 -v -f minim.mdp -c 6LYZ.gro -p 6LYZ.top -o
6LYZ-EM-vacuum.tpr
mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-vacuum


3. Periodic boundary conditions
editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -d 0.75 -box
7.0 7.0 7.0

4. Add another 20 ligands randomly into the simulation (nm^3) box
genbox_mpi -seed 201 -cp 6LYZ-PBC.gro -ci ligand.gro -nmol 20 -p 6LYZ.top -o
6LYZ20ligand.gro

6. Solvent addition
genbox_mpi -cp 6LYZ20ligand.gro -cs spc216.gro -p 6LYZ.top -o 6LYZ-water.gro

7. Addition of ions: counter charge and concentration
grompp_mpi -v -f minim.mdp -c 6LYZ-water.gro -p 6LYZ.top -o 6LYZ-water.tpr
genion_mpi -s 6LYZ-water.tpr -o 6LYZ-solvated.gro -nn 28 -nname CL-

8. Energy minimization of the solvated system
pbc = xyz (minim.mdp)
grompp_mpi -np 16 -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o
6LYZ-EM-solvated
mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-solvated


Reading file 6LYZ-EM-solvated.tpr, VERSION 3.3.3 (single precision)
Reading file 6LYZ-EM-solvated.tpr, VERSION 3.3.3 (single precision)
6LYZ-EM-solvated.tpr:
   header:
      bIr    = present
      bBox   = present
      bTop   = present
      bX     = present
      bV     = present
      bF     = not present
      natoms = 33042
      step   = 0
      t      = 0.000000e+00
      lambda = 0.000000e+00
   ir:
      integrator           = steep
      nsteps               = 50000
      init_step            = 0
      ns_type              = Simple
      nstlist              = 5
      ndelta               = 2
      bDomDecomp           = FALSE
      decomp_dir           = 0
      nstcomm              = 1
      comm_mode            = Linear
      nstcheckpoint        = 1000
      nstlog               = 100
      nstxout              = 100
      nstvout              = 100
      nstfout              = 0
      nstenergy            = 1
      nstxtcout            = 0
      init_t               = 0
      delta_t              = 0.001
      xtcprec              = 1000
      nkx                  = 0
      nky                  = 0
      nkz                  = 0
      pme_order            = 4
      ewald_rtol           = 1e-05
      ewald_geometry       = 0
      epsilon_surface      = 0
      optimize_fft         = FALSE
      ePBC                 = xyz
      bUncStart            = FALSE
      bShakeSOR            = FALSE
      etc                  = No
      epc                  = No
      epctype              = Isotropic
      tau_p                = 1
      ref_p (3x3):
         ref_p[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
         ref_p[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
         ref_p[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      compress (3x3):
         compress[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
         compress[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
         compress[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      andersen_seed        = 815131
      rlist                = 1
      coulombtype          = Cut-off
      rcoulomb_switch      = 0
      rcoulomb             = 1
      vdwtype              = Cut-off
      rvdw_switch          = 0
      rvdw                 = 1
      epsilon_r            = 1
      epsilon_rf           = 1
      tabext               = 1
      gb_algorithm         = Still
      nstgbradii           = 1
      rgbradii             = 2
      gb_saltconc          = 0
      implicit_solvent     = No
      DispCorr             = No
      fudgeQQ              = 1
      free_energy          = no
      init_lambda          = 0
      sc_alpha             = 0
      sc_power             = 0
      sc_sigma             = 0.3
      delta_lambda         = 0
      disre_weighting      = Conservative
      disre_mixed          = FALSE
      dr_fc                = 1000
      dr_tau               = 0
      nstdisreout          = 100
      orires_fc            = 0
      orires_tau           = 0
      nstorireout          = 100
      dihre-fc             = 1000
      dihre-tau            = 0
      nstdihreout          = 100
      em_stepsize          = 0.01
      em_tol               = 1
      niter                = 20
      fc_stepsize          = 0
      nstcgsteep           = 1000
      nbfgscorr            = 10
      ConstAlg             = Lincs
      shake_tol            = 0.0001
      lincs_order          = 4
      lincs_warnangle      = 30
      lincs_iter           = 1
      bd_fric              = 0
      ld_seed              = 1993
      cos_accel            = 0
      deform (3x3):
         deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
         deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
         deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      userint1             = 0
      userint2             = 0
      userint3             = 0
      userint4             = 0
      userreal1            = 0
      userreal2            = 0
      userreal3            = 0
      userreal4            = 0
grpopts:
      nrdf:            99123
      ref_t:               0
      tau_t:               0
anneal:                   No
ann_npoints:               0
      acc:                 0           0           0
      nfreeze:           N           N           N
      energygrp_flags[  0]: 0
      efield-x:
         n = 0
      efield-xt:
         n = 0
      efield-y:
         n = 0
      efield-yt:
         n = 0
      efield-z:
         n = 0
      efield-zt:
         n = 0
      bQMMM                = FALSE
      QMconstraints        = 0
      QMMMscheme           = 0
      scalefactor          = 1
qm_opts:
      ngQM                 = 0
   box (3x3):
      box[    0]={ 7.00000e+00,  0.00000e+00,  0.00000e+00}
      box[    1]={ 0.00000e+00,  7.00000e+00,  0.00000e+00}
      box[    2]={ 0.00000e+00,  0.00000e+00,  7.00000e+00}
   boxv (3x3):
      boxv[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      boxv[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      boxv[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   pcoupl_mu (3x3):
      pcoupl_mu[    0]={ 1.00000e+00,  0.00000e+00,  0.00000e+00}
      pcoupl_mu[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
      pcoupl_mu[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}
   nosehoover_xi:                  0
   x (33042x3):
      x[    0]={ 3.88200e+00,  2.44200e+00,  2.61100e+00}
      x[    1]={ 3.87900e+00,  2.34300e+00,  2.62700e+00}
      x[    2]={ 3.97600e+00,  2.47000e+00,  2.59300e+00}
      x[    3]={ 3.85000e+00,  2.49000e+00,  2.69300e+00}
      x[    4]={ 3.79500e+00,  2.47800e+00,  2.49600e+00}
      x[    5]={ 3.65000e+00,  2.43700e+00,  2.52700e+00}
      x[    6]={ 3.55300e+00,  2.46400e+00,  2.41200e+00}
      x[    7]={ 3.41000e+00,  2.42200e+00,  2.44600e+00}
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