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Peptide expulsed from Bilayer
- Alvaro
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1 year 2 months ago #9606
by Alvaro
Peptide expulsed from Bilayer was created by Alvaro
Hello everyone.
I know this is not the forum for this, but I have a question that I would really like to resolve.
I am fairly new to the use of martini and have managed to build several membranes (different compositions and dynamic parameters) to test the affinity and curvature that certain peptides could effect on these membranes.
I have efficiently achieved results, however, from time to time something peculiar occurs that I would like to ask you.
Depending on the amount of peptides and, in turn, the peptide, these escape from the membrane (assuming that it starts with the peptide inserted in the center of the membrane or, failing that, several peptides inserted inside the membrane at a standard distance between each other). they). There is any error? Is this type of disruption normal? Should I place some type of movement restriction? Does this correspond to an acceptable membrane disruption parameter? Is it a perse result?
; minim.mdp - used as input into grompp to generate em.tpr
define = -DFLEXIBLE
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 100 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.00001 ; Energy step size
nsteps = 500000 ; Maximum number of (minimization) steps to perform
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 20 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = reaction-field ; Treatment of long range electrostatic interactions
rcoulomb = 1.2 ; Short-range electrostatic cut-off
rvdw = 1.2 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
epsilon_r = 15 ; Relative dielectric constant, 2.5 with polarizable water or 15 with classic martini
epsilon_rf = 0 ; Relative dielectric constant of the reaction field - 0 means infinity
verlet-buffer-tolerance = 0.005 ; Default 0.005, only with Verlet scheme, maximum allowed error for pair interactions per particles
define = -DPOSRES -DBILAYER_LIPIDHEAD_FC=100
; Run parameters
integrator = md ; leap-frog integrator
; nsteps = 5000 ; Limit Testing
nsteps = 10000000 ; 2 * 5000000 = 10 ns -- 500.000 -> 1 ns
dt = 0.01 ; 2 fs
comm-mode = none
; Output control
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstlog = 1000
nstenergy = 1000
nstxout-compressed = 1000
compressed-x-precision = 1000
; Bond parameters
constraints = none
constraint-algorithm = lincs
; Nonbonded settings
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 20 ; 20 fs, largely irrelevant with Verlet
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
epsilon_r = 15
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
DispCorr = EnerPres ; account for cut-off vdW scheme
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Bilayer Solvent Protein ; two coupling groups - more accurate
tau_t = 1.0 1.0 1.0 ; time constant, in ps
ref_t = 310 310 310 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = berendsen ; Pressure coupling on in NPT
pcoupltype = semiisotropic ; uniform scaling of box vectors
tau_p = 4.0 ; time constant, in ps
ref_p = 1.0 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility of water, bar^-1
refcoord_scaling = all
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 310 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
; Run parameters
integrator = md ; leap-frog integrator
; nsteps = 5000 ; Limit Testing
nsteps = 80000000 ; 2 * 5000000 = 10 ns -- 500.000 -> 1 ns
dt = 0.025 ; 2 fs
nstcomm = 1
comm-mode = linear
comm-grps = Bilayer Solvent Protein
; Output control
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstlog = 1000
nstenergy = 1000
nstxout-compressed = 1000
compressed-x-precision = 1000
; Bond parameters
continuation = yes ; Restarting after NVT
constraints = none
constraint-algorithm = Lincs
; Nonbonded settings
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 20 ; 20 fs, largely irrelevant with Verlet
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
epsilon_r = 15
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
DispCorr = EnerPres ; account for cut-off vdW scheme
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Bilayer Solvent Protein ; two coupling groups - more accurate
tau_t = 1.0 1.0 1.0 ; time constant, in ps
ref_t = 310 310 310 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = berendsen ; Pressure coupling on in NPT
pcoupltype = semiisotropic ; uniform scaling of box vectors
tau_p = 4.0 ; time constant, in ps
ref_p = 1.0 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility of water, bar^-1
refcoord_scaling = all
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Velocity generation
gen_vel = no ; Velocity generation is off
I know this is not the forum for this, but I have a question that I would really like to resolve.
I am fairly new to the use of martini and have managed to build several membranes (different compositions and dynamic parameters) to test the affinity and curvature that certain peptides could effect on these membranes.
I have efficiently achieved results, however, from time to time something peculiar occurs that I would like to ask you.
Depending on the amount of peptides and, in turn, the peptide, these escape from the membrane (assuming that it starts with the peptide inserted in the center of the membrane or, failing that, several peptides inserted inside the membrane at a standard distance between each other). they). There is any error? Is this type of disruption normal? Should I place some type of movement restriction? Does this correspond to an acceptable membrane disruption parameter? Is it a perse result?
Minimization Parameters
[ Click to expand ]
[ Click to hide ]
; minim.mdp - used as input into grompp to generate em.tpr
define = -DFLEXIBLE
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 100 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.00001 ; Energy step size
nsteps = 500000 ; Maximum number of (minimization) steps to perform
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 20 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = reaction-field ; Treatment of long range electrostatic interactions
rcoulomb = 1.2 ; Short-range electrostatic cut-off
rvdw = 1.2 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
epsilon_r = 15 ; Relative dielectric constant, 2.5 with polarizable water or 15 with classic martini
epsilon_rf = 0 ; Relative dielectric constant of the reaction field - 0 means infinity
verlet-buffer-tolerance = 0.005 ; Default 0.005, only with Verlet scheme, maximum allowed error for pair interactions per particles
Equilibration Parameters
[ Click to expand ]
[ Click to hide ]
define = -DPOSRES -DBILAYER_LIPIDHEAD_FC=100
; Run parameters
integrator = md ; leap-frog integrator
; nsteps = 5000 ; Limit Testing
nsteps = 10000000 ; 2 * 5000000 = 10 ns -- 500.000 -> 1 ns
dt = 0.01 ; 2 fs
comm-mode = none
; Output control
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstlog = 1000
nstenergy = 1000
nstxout-compressed = 1000
compressed-x-precision = 1000
; Bond parameters
constraints = none
constraint-algorithm = lincs
; Nonbonded settings
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 20 ; 20 fs, largely irrelevant with Verlet
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
epsilon_r = 15
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
DispCorr = EnerPres ; account for cut-off vdW scheme
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Bilayer Solvent Protein ; two coupling groups - more accurate
tau_t = 1.0 1.0 1.0 ; time constant, in ps
ref_t = 310 310 310 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = berendsen ; Pressure coupling on in NPT
pcoupltype = semiisotropic ; uniform scaling of box vectors
tau_p = 4.0 ; time constant, in ps
ref_p = 1.0 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility of water, bar^-1
refcoord_scaling = all
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 310 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
Production Run
[ Click to expand ]
[ Click to hide ]
; Run parameters
integrator = md ; leap-frog integrator
; nsteps = 5000 ; Limit Testing
nsteps = 80000000 ; 2 * 5000000 = 10 ns -- 500.000 -> 1 ns
dt = 0.025 ; 2 fs
nstcomm = 1
comm-mode = linear
comm-grps = Bilayer Solvent Protein
; Output control
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstlog = 1000
nstenergy = 1000
nstxout-compressed = 1000
compressed-x-precision = 1000
; Bond parameters
continuation = yes ; Restarting after NVT
constraints = none
constraint-algorithm = Lincs
; Nonbonded settings
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 20 ; 20 fs, largely irrelevant with Verlet
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
epsilon_r = 15
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
DispCorr = EnerPres ; account for cut-off vdW scheme
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Bilayer Solvent Protein ; two coupling groups - more accurate
tau_t = 1.0 1.0 1.0 ; time constant, in ps
ref_t = 310 310 310 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = berendsen ; Pressure coupling on in NPT
pcoupltype = semiisotropic ; uniform scaling of box vectors
tau_p = 4.0 ; time constant, in ps
ref_p = 1.0 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility of water, bar^-1
refcoord_scaling = all
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Velocity generation
gen_vel = no ; Velocity generation is off
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