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Martini 3 Density Profile is oscillatory
- arthurmluz
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2 weeks 5 days ago #9743
by arthurmluz
Martini 3 Density Profile is oscillatory was created by arthurmluz
Hi everyone!
I've been using Martini 3 to model a simple water/hexadecane interfacial system and I've noticed some oscillatory spikes in the density profile for my system.
Sometimes, water density jumps to close to 1100 kg/m3 in a slab and goes back to normal. Is this expected?
Here's the mdp file:
; STANDARD MD INPUT OPTIONS FOR MARTINI 3.x
; Updated 30 Jan 2017 by PCTS
;
; for use with GROMACS 5
; TIMESTEP IN MARTINI
; Default timestep of 20 fs.
integrator = md
dt = 0.02
nsteps = 2000000
nstcomm = 100
comm-grps =
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxout-compressed = 1000
compressed-x-precision = 100
compressed-x-grps =
;energygrps = Group1 Group2
; NEIGHBOURLIST and MARTINI
; To achieve faster simulations in combination with the Verlet-neighborlist
; scheme, Martini can be simulated with a straight cutoff. In order to
; do so, the cutoff distance is reduced 1.1 nm.
; Neighborlist length should be optimized depending on your hardware setup:
; updating ever 20 steps should be fine for classic systems, while updating
; every 30-40 steps might be better for GPU based systems.
; The Verlet neighborlist scheme will automatically choose a proper neighborlist
; length, based on a energy drift tolerance.
;
; Coulomb interactions can alternatively be treated using a reaction-field,
; giving slightly better properties.
; Please realize that electrostVatic interactions in the Martini model are
; not considered to be very accurate to begin with, especially as the
; screening in the system is set to be uniform across the system with
; a screening constant of 15. When using PME, please make sure your
; system properties are still reasonable.
;
; With the polarizable water model, the relative electrostatic screening
; (epsilon_r) should have a value of 2.5, representative of a low-dielectric
; apolar solvent. The polarizable water itself will perform the explicit screening
; in aqueous environment. In this case, the use of PME is more realistic.
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005
coulombtype = reaction-field
rcoulomb = 1.1
epsilon_r = 15 ; 2.5 (with polarizable water)
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1
; MARTINI and TEMPERATURE/PRESSURE
; normal temperature and pressure coupling schemes can be used.
; It is recommended to couple individual groups in your system separately.
; Good temperature control can be achieved with the velocity rescale (V-rescale)
; thermostat using a coupling constant of the order of 1 ps. Even better
; temperature control can be achieved by reducing the temperature coupling
; constant to 0.1 ps, although with such tight coupling (approaching
; the time step) one can no longer speak of a weak-coupling scheme.
; We therefore recommend a coupling time constant of at least 0.5 ps.
; The Berendsen thermostat is less suited since it does not give
; a well described thermodynamic ensemble.
;
; Pressure can be controlled with the Parrinello-Rahman barostat,
; with a coupling constant in the range 4-8 ps and typical compressibility
; in the order of 10e-4 - 10e-5 bar-1. Note that, for equilibration purposes,
; the Berendsen barostat probably gives better results, as the Parrinello-
; Rahman is prone to oscillating behaviour. For bilayer systems the pressure
; coupling should be done semiisotropic.
tcoupl = v-rescale
tc-grps = SYSTEM
tau_t = 1.0
ref_t = 300
Pcoupl = c-rescale
Pcoupltype = semiisotropic
tau_p = 4.0 4.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422
compressibility = 0.0 3e-4
ref_p = 1.0 1.0
gen_vel = no
gen_temp = 310
gen_seed = 473529
; MARTINI and CONSTRAINTS
; for ring systems and stiff bonds constraints are defined
; which are best handled using Lincs.
constraints = none
constraint_algorithm = Lincs
; With Polarizable water:
; lincs_warnangle = 90
I've been using Martini 3 to model a simple water/hexadecane interfacial system and I've noticed some oscillatory spikes in the density profile for my system.
Sometimes, water density jumps to close to 1100 kg/m3 in a slab and goes back to normal. Is this expected?
Here's the mdp file:
; STANDARD MD INPUT OPTIONS FOR MARTINI 3.x
; Updated 30 Jan 2017 by PCTS
;
; for use with GROMACS 5
; TIMESTEP IN MARTINI
; Default timestep of 20 fs.
integrator = md
dt = 0.02
nsteps = 2000000
nstcomm = 100
comm-grps =
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxout-compressed = 1000
compressed-x-precision = 100
compressed-x-grps =
;energygrps = Group1 Group2
; NEIGHBOURLIST and MARTINI
; To achieve faster simulations in combination with the Verlet-neighborlist
; scheme, Martini can be simulated with a straight cutoff. In order to
; do so, the cutoff distance is reduced 1.1 nm.
; Neighborlist length should be optimized depending on your hardware setup:
; updating ever 20 steps should be fine for classic systems, while updating
; every 30-40 steps might be better for GPU based systems.
; The Verlet neighborlist scheme will automatically choose a proper neighborlist
; length, based on a energy drift tolerance.
;
; Coulomb interactions can alternatively be treated using a reaction-field,
; giving slightly better properties.
; Please realize that electrostVatic interactions in the Martini model are
; not considered to be very accurate to begin with, especially as the
; screening in the system is set to be uniform across the system with
; a screening constant of 15. When using PME, please make sure your
; system properties are still reasonable.
;
; With the polarizable water model, the relative electrostatic screening
; (epsilon_r) should have a value of 2.5, representative of a low-dielectric
; apolar solvent. The polarizable water itself will perform the explicit screening
; in aqueous environment. In this case, the use of PME is more realistic.
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005
coulombtype = reaction-field
rcoulomb = 1.1
epsilon_r = 15 ; 2.5 (with polarizable water)
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1
; MARTINI and TEMPERATURE/PRESSURE
; normal temperature and pressure coupling schemes can be used.
; It is recommended to couple individual groups in your system separately.
; Good temperature control can be achieved with the velocity rescale (V-rescale)
; thermostat using a coupling constant of the order of 1 ps. Even better
; temperature control can be achieved by reducing the temperature coupling
; constant to 0.1 ps, although with such tight coupling (approaching
; the time step) one can no longer speak of a weak-coupling scheme.
; We therefore recommend a coupling time constant of at least 0.5 ps.
; The Berendsen thermostat is less suited since it does not give
; a well described thermodynamic ensemble.
;
; Pressure can be controlled with the Parrinello-Rahman barostat,
; with a coupling constant in the range 4-8 ps and typical compressibility
; in the order of 10e-4 - 10e-5 bar-1. Note that, for equilibration purposes,
; the Berendsen barostat probably gives better results, as the Parrinello-
; Rahman is prone to oscillating behaviour. For bilayer systems the pressure
; coupling should be done semiisotropic.
tcoupl = v-rescale
tc-grps = SYSTEM
tau_t = 1.0
ref_t = 300
Pcoupl = c-rescale
Pcoupltype = semiisotropic
tau_p = 4.0 4.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422
compressibility = 0.0 3e-4
ref_p = 1.0 1.0
gen_vel = no
gen_temp = 310
gen_seed = 473529
; MARTINI and CONSTRAINTS
; for ring systems and stiff bonds constraints are defined
; which are best handled using Lincs.
constraints = none
constraint_algorithm = Lincs
; With Polarizable water:
; lincs_warnangle = 90
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