[gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3
Chih-Ying Lin
chihying2008 at gmail.com
Fri Jan 1 23:38:09 CET 2010
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
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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