[gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3
Chih-Ying Lin
chihying2008 at gmail.com
Fri Jan 1 23:33:40 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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