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Domain decomposition error
- bt12d026
- Topic Author
- Visitor
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
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- xavier
- Offline
- Admin
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
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