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}
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php