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DPPC vesicle simulation
- xuji06
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14 years 2 weeks ago #338
by xuji06
DPPC vesicle simulation was created by xuji06
I do the simulation as RAMDOM-I in the thesis "Molecular Dynamics Simulation of
the Formation, Structure, and Dynamics of Small Phospholipid Vesicles"
using martini_v2.0.itp force field. But I always get the micelles not the vesicles.
The topology file I use is as follows:
#include "martini_v2.0.itp"
#include "martini_v2.0_lipids.itp"
[ system ]
dppc_1500
[ molecules ]
DPPC 1500
W 360119
And the mdp file is:
title = DPPC_ARRAY
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0.0
dt = 0.025
nsteps = 5000000 ; 125ns
; number of steps for center of mass motion removal =
nstcomm = 1
comm-grps = System
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 5000 ;100ps
nstvout = 5000 ;100ps
nstfout = 5000 ;100ps
; Output frequency for energies to log file and energy file =
nstlog = 1000 ;20ps
nstenergy = 1000 ;20ps
; Output frequency and precision for xtc file =
nstxtcout = 5000 ;125ps
xtc_precision = 100
; 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 = DPPC W
; 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 = 1.4
; 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 = 20 ; or 15
; Method for doing Van der Waals
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = DPPC W
; Time constant (ps) and reference temperature (K) =
tau_t = 2 2
ref_t = 323 323
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 2.5
compressibility = 3e-5
ref_p = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = No
gen_temp = 323
gen_seed = 473529
; 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
Can someone help me whether there're something wrong in my top and mdp files?
And I also have another question. When I use the Gromacs genbox tool with the option -maxsol, i.e.
genbox_d -cp 1024_minimised.gro -cs water_323.gro -o waterbox.gro -maxsol 4224
there're only one part of the box space has waters. How can I fill the box with the given number of waters?
the Formation, Structure, and Dynamics of Small Phospholipid Vesicles"
using martini_v2.0.itp force field. But I always get the micelles not the vesicles.
The topology file I use is as follows:
#include "martini_v2.0.itp"
#include "martini_v2.0_lipids.itp"
[ system ]
dppc_1500
[ molecules ]
DPPC 1500
W 360119
And the mdp file is:
title = DPPC_ARRAY
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0.0
dt = 0.025
nsteps = 5000000 ; 125ns
; number of steps for center of mass motion removal =
nstcomm = 1
comm-grps = System
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 5000 ;100ps
nstvout = 5000 ;100ps
nstfout = 5000 ;100ps
; Output frequency for energies to log file and energy file =
nstlog = 1000 ;20ps
nstenergy = 1000 ;20ps
; Output frequency and precision for xtc file =
nstxtcout = 5000 ;125ps
xtc_precision = 100
; 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 = DPPC W
; 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 = 1.4
; 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 = 20 ; or 15
; Method for doing Van der Waals
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = DPPC W
; Time constant (ps) and reference temperature (K) =
tau_t = 2 2
ref_t = 323 323
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 2.5
compressibility = 3e-5
ref_p = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = No
gen_temp = 323
gen_seed = 473529
; 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
Can someone help me whether there're something wrong in my top and mdp files?
And I also have another question. When I use the Gromacs genbox tool with the option -maxsol, i.e.
genbox_d -cp 1024_minimised.gro -cs water_323.gro -o waterbox.gro -maxsol 4224
there're only one part of the box space has waters. How can I fill the box with the given number of waters?
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- xavier
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14 years 2 weeks ago #339
by xavier
Replied by xavier on topic DPPC vesicle simulation
Well, nothing looks fundamentally wrong. Could you precise the source (author/university) of the thesis work you mention? It could be interesting to contact the authors directly.
XAvier
XAvier
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- mara
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14 years 2 weeks ago #340
by mara
I might be wrong, but I think an older version of Martini was used in that study. Even small changes in the interaction matrix may result in the formation of different phases. Maybe you are hitting this? Or maybe you're just unlucky! ;)
As Xavier already said, your .mdp file seems just fine.
I'd guess the water in water_323.gro are spatial ordered, i.e. the first 4224 water molecules are all located in the same region. Try adding single W with -ci or remove the surplus water e.g. with the zap.py script available from here: http://md.chem.rug.nl/~mara/softa/
-martti-
Replied by mara on topic DPPC vesicle simulation
xuji06 wrote: I do the simulation as RAMDOM-I in the thesis "Molecular Dynamics Simulation of
the Formation, Structure, and Dynamics of Small Phospholipid Vesicles"
using martini_v2.0.itp force field. But I always get the micelles not the vesicles.
I might be wrong, but I think an older version of Martini was used in that study. Even small changes in the interaction matrix may result in the formation of different phases. Maybe you are hitting this? Or maybe you're just unlucky! ;)
xuji06 wrote: Can someone help me whether there're something wrong in my top and mdp files?
As Xavier already said, your .mdp file seems just fine.
xuji06 wrote: And I also have another question. When I use the Gromacs genbox tool with the option -maxsol, i.e.
genbox_d -cp 1024_minimised.gro -cs water_323.gro -o waterbox.gro -maxsol 4224
there're only one part of the box space has waters. How can I fill the box with the given number of waters?
I'd guess the water in water_323.gro are spatial ordered, i.e. the first 4224 water molecules are all located in the same region. Try adding single W with -ci or remove the surplus water e.g. with the zap.py script available from here: http://md.chem.rug.nl/~mara/softa/
-martti-
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- durbignon
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14 years 2 weeks ago #341
by durbignon
Replied by durbignon on topic DPPC vesicle simulation
You should probably also have a critical look at the Lipid/Water ratio.
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- xuji06
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14 years 2 weeks ago #344
by xuji06
Replied by xuji06 on topic DPPC vesicle simulation
Thank you for all your help!
I'll check the simulation and have a try
with the old MARTINI force field.
I'll check the simulation and have a try
with the old MARTINI force field.
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