[gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3
Mark Abraham
Mark.Abraham at anu.edu.au
Fri Jan 1 23:50:44 CET 2010
Chih-Ying Lin wrote:
>
>
>
>
> Hi
> Sorry that i have posted the same message for several times.
>
> 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
-d and -box are mutually exclusive. I'd have thought editconf would warn
about this. Anyway, pick one of them as a suitable value, and use only it.
> 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
Check this structure and the PBC cell visually for atomic overlaps.
There shouldn't be any...
> 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
Otherwise, looks OK. Your use of plain cutoffs in your .mdp is probably
OK for EM, but is antiquated for anything else. Be sure to understand
all the output from grompp - particularly errors, warnings and notes.
Concatenating the above commands into a shell script is often a very
good idea. Not only can you be sure you're doing the "same thing" when
you go to run some variation next time, but it's partly self-documenting
and self-recording.
Just as the GROMACS installation guides tell you, there's no value in
compiling programs other than mdrun with MPI. It doesn't hurt to do so,
however, so long as your compute environment is sufficiently homogeneous.
If you're really sure about using 3.3.3, you will want to investigate
using grompp -sort and -shuffle. See man page and wiki docs.
Mark
> 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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