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CG simuation of a polymer crashes with DD
- Mousumi
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9 years 6 months ago #4095
by Mousumi
CG simuation of a polymer crashes with DD was created by Mousumi
Hi,
Good evening!
I am trying to simulate a single chain of a polymer conjugated with a drug molecule using CG-approach. I selected a snap from the all-atom simulation of around 1.5ns and then mapped it into the CG configuration. The polymer is solvated in a box of water beads. Energy minimizations runs properly. However when I am trying to do the equilibration the simulations are crashing with the error below.
##############################################################################################
Not all bonded interactions have been properly assigned to the domain decomposition cells
A list of missing interactions:
G96Angle of 730 missing 2
Molecule type 'CellaxDTX'
the first 10 missing interactions, except for exclusions:
G96Angle atoms 253 255 261 global 253 255 261
G96Angle atoms 254 255 261 global 254 255 261
Program mdrun, VERSION 4.6.5
Source code file: /usr/local/src/gromacs-4.6.5/src/mdlib/domdec_top.c, line: 393
Fatal error:
2 of the 1272 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.6 nm) or the two-body cut-off distance (1.6 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
####################################################################################################
After doing thorough searches in Gromacs forum as well as Martini forum I found the most prescribed solution was to increas -rdd value. So I used a range of -rdd values from 1.25 to 2.5. However it crashes again with the same error. For equlibration I have changed integration time step from .005 to .002 and same for production run (.025-.002). Reducing the time steps equilibration runs for 50000 steps but crashed again when further extended for equilibration or production run. I then started from the begining with completely new starting structure. the same error appeared again. Changing Pcoupl did not help either. I could not find any other solution to fix this problem. Could anyone kindly help me in this regard? I would be highly grateful to you. For the note: I have already run successfully the CG simulation of the same polymer and same drug of different composition. The mdp files for minimization, equilibration and production run are given below:
min.mdp file:
integrator = steep
tinit = 0.0
dt = 0.005
nsteps = 50000
nstlog = 500
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.2
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
equlibration.mdp options are:
integrator = md
dt = 0.002
nsteps = 50000
nstcomm = 10
nstcalcenergy = 5
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstlog = 1000
nstenergy = 25
nstxtcout = 25
xtc_precision = 100
energygrps = system
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.2
coulombtype = Shift ;Reaction_field ;For use with Verlet-pairlist
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift ;cutoff ;For use with Verlet-pairlist
rvdw_switch = 0.9
rvdw = 1.2
tcoupl = v-rescale ; modified Berendsen thermostat
tc-grps = polymer W
tau_t = 1.0 1.0
ref_t = 300 300
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p = 8.0
compressibility = 3e-4
ref_p = 1.0
gen_vel = yes
gen_temp = 300
gen_seed = -1
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
Production run mdp options:
integrator = md
tinit = 0.0
dt = 0.005
nsteps = 500000 ;1000000
nstcomm = 1
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 1000
nstenergy = 1000
nstxtcout = 5000
xtc_precision = 1000
nstcalcenergy = 10
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = polymer W
tau_t = 0.3 0.3
ref_t = 300 300
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 3.0
compressibility = 3e-5
ref_p = 1.0
gen_vel = no
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
Good evening!
I am trying to simulate a single chain of a polymer conjugated with a drug molecule using CG-approach. I selected a snap from the all-atom simulation of around 1.5ns and then mapped it into the CG configuration. The polymer is solvated in a box of water beads. Energy minimizations runs properly. However when I am trying to do the equilibration the simulations are crashing with the error below.
##############################################################################################
Not all bonded interactions have been properly assigned to the domain decomposition cells
A list of missing interactions:
G96Angle of 730 missing 2
Molecule type 'CellaxDTX'
the first 10 missing interactions, except for exclusions:
G96Angle atoms 253 255 261 global 253 255 261
G96Angle atoms 254 255 261 global 254 255 261
Program mdrun, VERSION 4.6.5
Source code file: /usr/local/src/gromacs-4.6.5/src/mdlib/domdec_top.c, line: 393
Fatal error:
2 of the 1272 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.6 nm) or the two-body cut-off distance (1.6 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
####################################################################################################
After doing thorough searches in Gromacs forum as well as Martini forum I found the most prescribed solution was to increas -rdd value. So I used a range of -rdd values from 1.25 to 2.5. However it crashes again with the same error. For equlibration I have changed integration time step from .005 to .002 and same for production run (.025-.002). Reducing the time steps equilibration runs for 50000 steps but crashed again when further extended for equilibration or production run. I then started from the begining with completely new starting structure. the same error appeared again. Changing Pcoupl did not help either. I could not find any other solution to fix this problem. Could anyone kindly help me in this regard? I would be highly grateful to you. For the note: I have already run successfully the CG simulation of the same polymer and same drug of different composition. The mdp files for minimization, equilibration and production run are given below:
min.mdp file:
integrator = steep
tinit = 0.0
dt = 0.005
nsteps = 50000
nstlog = 500
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.2
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
equlibration.mdp options are:
integrator = md
dt = 0.002
nsteps = 50000
nstcomm = 10
nstcalcenergy = 5
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstlog = 1000
nstenergy = 25
nstxtcout = 25
xtc_precision = 100
energygrps = system
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.2
coulombtype = Shift ;Reaction_field ;For use with Verlet-pairlist
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift ;cutoff ;For use with Verlet-pairlist
rvdw_switch = 0.9
rvdw = 1.2
tcoupl = v-rescale ; modified Berendsen thermostat
tc-grps = polymer W
tau_t = 1.0 1.0
ref_t = 300 300
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p = 8.0
compressibility = 3e-4
ref_p = 1.0
gen_vel = yes
gen_temp = 300
gen_seed = -1
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
Production run mdp options:
integrator = md
tinit = 0.0
dt = 0.005
nsteps = 500000 ;1000000
nstcomm = 1
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 1000
nstenergy = 1000
nstxtcout = 5000
xtc_precision = 1000
nstcalcenergy = 10
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = polymer W
tau_t = 0.3 0.3
ref_t = 300 300
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 3.0
compressibility = 3e-5
ref_p = 1.0
gen_vel = no
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
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- xavier
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- Posts: 416
9 years 6 months ago #4103
by xavier
Replied by xavier on topic CG simuation of a polymer crashes with DD
When running mdrun you can increase the minimum size for domain decomposition using the "rdd"option. For CG we generally use 1.6 to 1.8 nm.
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