- Posts: 211
Protein in water
- Norbert
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10 years 6 months ago #2284
by Norbert
Protein in water was created by Norbert
Hello,
I am studing a protein in water with Martini.
The initial system (protein+water) was build, minimized and heating until 310K by 50K steps of 100 ns.
Then I would like perform production of several micro second.
After several 100 ns, the run stops with a segmentation fault message.
The md.mdp file I uses is the following.
Please could you help me?
; VARIOUS PREPROCESSING OPTIONS =
title = Martini
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0.0
dt = 0.040
nsteps = 125000000
; number of steps for center of mass motion removal =
;nstcomm = 1
comm-grps = protein W ION
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 0
nstvout = 0
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 25000
nstenergy = 25000
; Output frequency and precision for xtc file =
nstxtcout = 25000
xtc_precision = 200
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps = protein W ION
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or none =
pbc = xyz
; nblist cut-off =
rlist = 1.2
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths =
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx = 10
fourier_ny = 10
fourier_nz = 10
; EWALD/PME/PPPM parameters =
pme_order = 4
ewald_rtol = 1e-05
epsilon_surface = 0
optimize_fft = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = v-rescale
; Groups to couple separately =
tc-grps = protein W ION
; Time constant (ps) and reference temperature (K) =
tau_t = 1.0 1.0 1.0
ref_t = 310 310 310
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 1.0
compressibility = 5e-5
ref_p = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 310
gen_seed = 42271550
; OPTIONS FOR BONDS =
constraints = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start = no
; Highest order in the expansion of the constraint coupling matrix =
lincs_order = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle = 30
Thank you very much
Norbert
I am studing a protein in water with Martini.
The initial system (protein+water) was build, minimized and heating until 310K by 50K steps of 100 ns.
Then I would like perform production of several micro second.
After several 100 ns, the run stops with a segmentation fault message.
The md.mdp file I uses is the following.
Please could you help me?
; VARIOUS PREPROCESSING OPTIONS =
title = Martini
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0.0
dt = 0.040
nsteps = 125000000
; number of steps for center of mass motion removal =
;nstcomm = 1
comm-grps = protein W ION
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 0
nstvout = 0
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 25000
nstenergy = 25000
; Output frequency and precision for xtc file =
nstxtcout = 25000
xtc_precision = 200
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps = protein W ION
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or none =
pbc = xyz
; nblist cut-off =
rlist = 1.2
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths =
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx = 10
fourier_ny = 10
fourier_nz = 10
; EWALD/PME/PPPM parameters =
pme_order = 4
ewald_rtol = 1e-05
epsilon_surface = 0
optimize_fft = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = v-rescale
; Groups to couple separately =
tc-grps = protein W ION
; Time constant (ps) and reference temperature (K) =
tau_t = 1.0 1.0 1.0
ref_t = 310 310 310
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 1.0
compressibility = 5e-5
ref_p = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 310
gen_seed = 42271550
; OPTIONS FOR BONDS =
constraints = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start = no
; Highest order in the expansion of the constraint coupling matrix =
lincs_order = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle = 30
Thank you very much
Norbert
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- Clement
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10 years 6 months ago #2288
by Clement
Replied by Clement on topic Protein in water
My guess would be the timestep is a bit too big... But it's dependent on the size of the protein. Due to the complexity of the protein topologies (complicated bonded parameters everywhere), and it can be a mess to solve from one step to the other when the step is too large; and Seg Fault cause the program gives up.
Another comment about your parameters... Why are you not coupling the water and ions together? You might have a good reason, it's just I've not idea what you're studying...
Another comment about your parameters... Why are you not coupling the water and ions together? You might have a good reason, it's just I've not idea what you're studying...
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- Norbert
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Topic Author
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10 years 6 months ago #2289
by Norbert
Replied by Norbert on topic Protein in water
Thank you
the protein is a dimer 2x90 aa.
I am going to try with a 0.03 time step.
Thanks
Norbert
the protein is a dimer 2x90 aa.
I am going to try with a 0.03 time step.
Thanks
Norbert
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- Clement
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- Posts: 211
10 years 6 months ago #2290
by Clement
Replied by Clement on topic Protein in water
Depending on the secondary structure of your proteins, and depending on what you want to study of course, you might want to give a try to an elastic network approach...
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- Norbert
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10 years 6 months ago #2292
by Norbert
Replied by Norbert on topic Protein in water
The secondary structure of each monomer is the following
CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEECCCEEEEEEEECCEEEECCCCCCEEEECCEEEEEEEECHHHHHHCC
and I would like to study a partial separation of the two monomers.
CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEECCCEEEEEEEECCEEEECCCCCCEEEECCEEEEEEEECHHHHHHCC
and I would like to study a partial separation of the two monomers.
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- Clement
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- Posts: 211
10 years 6 months ago #2293
by Clement
Replied by Clement on topic Protein in water
I was more worried about beta sheets, but apparently you don't have any.
Unbinding, even partial, is tricky to study with Martini. First, there's no change of secondary structure allowed; second, the fine interactions often triggering such processes are... coarse in this case. But worth trying, we've seen examples!
Do you have experimental data to relate to? Kinetics of (un)binding...
Unbinding, even partial, is tricky to study with Martini. First, there's no change of secondary structure allowed; second, the fine interactions often triggering such processes are... coarse in this case. But worth trying, we've seen examples!
Do you have experimental data to relate to? Kinetics of (un)binding...
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