- Posts: 416
Domain decomposition error
- bt12d026
-
Topic Author
- Visitor
10 years 11 months ago #1585
by bt12d026
Domain decomposition error was created by bt12d026
Dear all,
I am performing a Protein in Water simulation according to the tutorial given in the site. But my simulation has stopped with the following error.
"Step 15407600: The domain decomposition grid has shifted too much in the Z-direction around cell 0 0 1"
I think there is some problem with my mdp options. Here is the content of my mdp file.
integrator = md
dt = 0.020
nsteps = 50000000
nstcomm = 10
comm-grps = System
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
xtc_precision = 100
xtc-grps = System
energygrps = Protein TRI PCW
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift ;Reaction_field (for use with Verlet-pairlist) ;PME (especially with polarizable water)
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15 ; 2.5 (with polarizable water)
vdw_type = Shift ;cutoff (for use with Verlet-pairlist)
rvdw_switch = 0.9
rvdw = 1.2 ;1.1 (for use with Verlet-pairlist)
tcoupl = v-rescale
tc-grps = Protein_TRI_PCW W_ION
tau_t = 1.0 1.0
ref_t = 310 310
pcoupl = Parrinello-Rahman
Pcoupltype = semiisotropic
tau_p = 12.0 12.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
gen_vel = no
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
Please help me if something is wrong with my mdp file.
Thanks for your valuable time and patience
I am performing a Protein in Water simulation according to the tutorial given in the site. But my simulation has stopped with the following error.
"Step 15407600: The domain decomposition grid has shifted too much in the Z-direction around cell 0 0 1"
I think there is some problem with my mdp options. Here is the content of my mdp file.
integrator = md
dt = 0.020
nsteps = 50000000
nstcomm = 10
comm-grps = System
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
xtc_precision = 100
xtc-grps = System
energygrps = Protein TRI PCW
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift ;Reaction_field (for use with Verlet-pairlist) ;PME (especially with polarizable water)
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15 ; 2.5 (with polarizable water)
vdw_type = Shift ;cutoff (for use with Verlet-pairlist)
rvdw_switch = 0.9
rvdw = 1.2 ;1.1 (for use with Verlet-pairlist)
tcoupl = v-rescale
tc-grps = Protein_TRI_PCW W_ION
tau_t = 1.0 1.0
ref_t = 310 310
pcoupl = Parrinello-Rahman
Pcoupltype = semiisotropic
tau_p = 12.0 12.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
gen_vel = no
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
Please help me if something is wrong with my mdp file.
Thanks for your valuable time and patience
Please Log in or Create an account to join the conversation.
- xavier
-
- Offline
- Admin
Less
More
10 years 11 months ago #1586
by xavier
Replied by xavier on topic Domain decomposition error
Why do you use semiisotropic pressure coupling? try to switch to isotropic ...
You probably see some deformation of the box ...
You probably see some deformation of the box ...
bt12d026 wrote: Dear all,
I am performing a Protein in Water simulation according to the tutorial given in the site. But my simulation has stopped with the following error.
"Step 15407600: The domain decomposition grid has shifted too much in the Z-direction around cell 0 0 1"
I think there is some problem with my mdp options. Here is the content of my mdp file.
integrator = md
dt = 0.020
nsteps = 50000000
nstcomm = 10
comm-grps = System
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
xtc_precision = 100
xtc-grps = System
energygrps = Protein TRI PCW
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift ;Reaction_field (for use with Verlet-pairlist) ;PME (especially with polarizable water)
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15 ; 2.5 (with polarizable water)
vdw_type = Shift ;cutoff (for use with Verlet-pairlist)
rvdw_switch = 0.9
rvdw = 1.2 ;1.1 (for use with Verlet-pairlist)
tcoupl = v-rescale
tc-grps = Protein_TRI_PCW W_ION
tau_t = 1.0 1.0
ref_t = 310 310
pcoupl = Parrinello-Rahman
Pcoupltype = semiisotropic
tau_p = 12.0 12.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
gen_vel = no
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
Please help me if something is wrong with my mdp file.
Thanks for your valuable time and patience
Please Log in or Create an account to join the conversation.
- bt12d026
-
Topic Author
- Visitor
10 years 11 months ago #1590
by bt12d026
Replied by bt12d026 on topic Domain decomposition error
Thank you sir. I will try and let you know if there is some problem.
Please Log in or Create an account to join the conversation.
Time to create page: 0.090 seconds