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choosing mdp file for lipid simulation
- shakira
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3 years 4 months ago #8776
by shakira
choosing mdp file for lipid simulation was created by shakira
Hi
I usually use the parameters of "martini_v2.x_new.mdp" given in martini downloads section for membrane simulations. Previously my membrane system includes lipid of similar head groups. Now I was trying to simulate a membrane system with lipids of different head groups (PE,PC,PG,CDL). With the "martini_v2.x_new.mdp" mdp file Gromacs gives following error:
Fatal error:
Step 7100: The total potential energy is -nan, which is not finite. The LJ and
electrostatic contributions to the energy are 0 and 0, respectively. A
non-finite potential energy can be caused by overlapping interactions in
bonded interactions or very large or Nan coordinate values. Usually this is
caused by a badly- or non-equilibrated initial configuration, incorrect
interactions or parameters in the topology.
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1[/color]
When I use "martini_v2.x_forcemod.mdp" the system runs without any error.
So vdw-modifier = force-switch works smoothly. So I m curious to know why it didnt work with vdw-modifier = Potential-shift-verlet. Doe it depend on the type of lipids in the system?
I usually use the parameters of "martini_v2.x_new.mdp" given in martini downloads section for membrane simulations. Previously my membrane system includes lipid of similar head groups. Now I was trying to simulate a membrane system with lipids of different head groups (PE,PC,PG,CDL). With the "martini_v2.x_new.mdp" mdp file Gromacs gives following error:
Fatal error:
Step 7100: The total potential energy is -nan, which is not finite. The LJ and
electrostatic contributions to the energy are 0 and 0, respectively. A
non-finite potential energy can be caused by overlapping interactions in
bonded interactions or very large or Nan coordinate values. Usually this is
caused by a badly- or non-equilibrated initial configuration, incorrect
interactions or parameters in the topology.
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1[/color]
When I use "martini_v2.x_forcemod.mdp" the system runs without any error.
So vdw-modifier = force-switch works smoothly. So I m curious to know why it didnt work with vdw-modifier = Potential-shift-verlet. Doe it depend on the type of lipids in the system?
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- saini
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2 years 6 months ago #9175
by saini
Replied by saini on topic choosing mdp file for lipid simulation
Hi Shakira,
I am also getting the same error (Fatal error:
Step 28561400: The total potential energy is nan, which is not finite. The LJ
and electrostatic contributions to the energy are 0 and -20416.1,
respectively. A non-finite potential energy can be caused by overlapping
interactions in bonded interactions or very large or Nan coordinate values.
Usually this is caused by a badly- or non-equilibrated initial configuration,
incorrect interactions or parameters in the topology.) during NPT equilibration.
My mdp file is this....
title = Martini
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 500000000 ; 1microsec
nstcomm = 100
comm-grps = cla_lipids sol
nstxout = 0
nstvout = 0
nstfout = 0
nstlog =100000
nstenergy =100000
nstxtcout =100000
xtc_precision =100000
xtc-grps = cla_lipids sol
cutoff-scheme = verlet
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.2
coulombtype = PME
pme-order = 4
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Cut-off
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = Berendsen
tc-grps = cla_lipids sol
tau_t = 2.0 2.0
ref_t = 293 293
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 1
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
gen_vel = no
gen_temp = 105
gen_seed = 548628
constraints = none
constraint_algorithm = Lincs
lincs_order = 4
lincs_warnangle = 30
Please suggest me something if you find out the solution of this error.
I am also getting the same error (Fatal error:
Step 28561400: The total potential energy is nan, which is not finite. The LJ
and electrostatic contributions to the energy are 0 and -20416.1,
respectively. A non-finite potential energy can be caused by overlapping
interactions in bonded interactions or very large or Nan coordinate values.
Usually this is caused by a badly- or non-equilibrated initial configuration,
incorrect interactions or parameters in the topology.) during NPT equilibration.
My mdp file is this....
title = Martini
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 500000000 ; 1microsec
nstcomm = 100
comm-grps = cla_lipids sol
nstxout = 0
nstvout = 0
nstfout = 0
nstlog =100000
nstenergy =100000
nstxtcout =100000
xtc_precision =100000
xtc-grps = cla_lipids sol
cutoff-scheme = verlet
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.2
coulombtype = PME
pme-order = 4
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Cut-off
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = Berendsen
tc-grps = cla_lipids sol
tau_t = 2.0 2.0
ref_t = 293 293
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 1
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
gen_vel = no
gen_temp = 105
gen_seed = 548628
constraints = none
constraint_algorithm = Lincs
lincs_order = 4
lincs_warnangle = 30
Please suggest me something if you find out the solution of this error.
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