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area per lipid
- syahidah
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11 years 10 months ago #994
by syahidah
area per lipid was created by syahidah
Dear all,
i have few problems with my result..
i run a simulation of 64 DPPC in water at 323K,
the simulation seems went well through the simulation,
except few molecules jumping out-in simulation box,but not many, only few..
the problem is, when i want to analyze my result, i found that my result is different with Prof Marrink's paper, whereas he got 0.62nm for the area per lipid and i get 0.9nm..
i try to re-run it, but the same result obtained..
may i know anyone here have any idea to solve this problem?...
Thank you and your cooperation is greatly appreciated..
best,
syahida
i have few problems with my result..
i run a simulation of 64 DPPC in water at 323K,
the simulation seems went well through the simulation,
except few molecules jumping out-in simulation box,but not many, only few..
the problem is, when i want to analyze my result, i found that my result is different with Prof Marrink's paper, whereas he got 0.62nm for the area per lipid and i get 0.9nm..
i try to re-run it, but the same result obtained..
may i know anyone here have any idea to solve this problem?...
Thank you and your cooperation is greatly appreciated..
best,
syahida
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- djurre
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11 years 10 months ago #996
by djurre
Replied by djurre on topic area per lipid
From 0.62 to 0.9 is a big difference. Did you check the pressure? Possibly the pressure (in the beginning of the simulation) is of, which means you should only analyze the last part of the simulation (and maybe simulate longer). Also, how did you setup the system? The system on the website has an equal number of lipids in both monolayers. Maybe in your system it is asymmetric?
If that doesn't solve your problem, please post the mdp-file content.
If that doesn't solve your problem, please post the mdp-file content.
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- syahidah
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11 years 10 months ago #997
by syahidah
Replied by syahidah on topic area per lipid
Hi Djurre,
this is my mdp file:
;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0
;
; for use with GROMACS 3.3
;
; VARIOUS PREPROCESSING OPTIONS =
title = Martini
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
; MARTINI - Most simulations are stable with dt=40 fs,
; some (especially rings) require 20-30 fs.
; The range of time steps used for parametrization
; is 20-40 fs, using smaller time steps is therefore not recommended.
integrator = md
; start time and timestep in ps
tinit = 0.0
dt = 0.030
nsteps = 17000000
; number of steps for center of mass motion removal =
nstcomm = 1
comm-grps =
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 5000
nstvout = 5000
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 1000
nstenergy = 1000
; Output frequency and precision for xtc file =
nstxtcout = 1000
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 =
; NEIGHBORSEARCHING PARAMETERS =
; MARTINI - no need for more frequent updates
; or larger neighborlist cut-off due
; to the use of shifted potential energy functions.
; 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
; OPTIONS FOR ELECTROSTATICS AND VDW =
; MARTINI - vdw and electrostatic interactions are used
; in their shifted forms. Changing to other types of
; electrostatics will affect the general performance of
; the model.
; 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
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; MARTINI - normal temperature and pressure coupling schemes
; can be used. It is recommended to couple individual groups
; in your system seperately.
; Temperature coupling =
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = DPPC W
; Time constant (ps) and reference temperature (K) =
tau_t = 0.3 0.3
ref_t = 323 323
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 3.0
compressibility = 3e-5
ref_p = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 323
gen_seed = 666
; OPTIONS FOR BONDS =
; MARTINI - for ring systems constraints are defined
; which are best handled using Lincs.
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
is it because i didn't do the heating/equilibration run first?
this is my mdp file:
;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0
;
; for use with GROMACS 3.3
;
; VARIOUS PREPROCESSING OPTIONS =
title = Martini
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
; MARTINI - Most simulations are stable with dt=40 fs,
; some (especially rings) require 20-30 fs.
; The range of time steps used for parametrization
; is 20-40 fs, using smaller time steps is therefore not recommended.
integrator = md
; start time and timestep in ps
tinit = 0.0
dt = 0.030
nsteps = 17000000
; number of steps for center of mass motion removal =
nstcomm = 1
comm-grps =
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 5000
nstvout = 5000
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 1000
nstenergy = 1000
; Output frequency and precision for xtc file =
nstxtcout = 1000
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 =
; NEIGHBORSEARCHING PARAMETERS =
; MARTINI - no need for more frequent updates
; or larger neighborlist cut-off due
; to the use of shifted potential energy functions.
; 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
; OPTIONS FOR ELECTROSTATICS AND VDW =
; MARTINI - vdw and electrostatic interactions are used
; in their shifted forms. Changing to other types of
; electrostatics will affect the general performance of
; the model.
; 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
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; MARTINI - normal temperature and pressure coupling schemes
; can be used. It is recommended to couple individual groups
; in your system seperately.
; Temperature coupling =
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = DPPC W
; Time constant (ps) and reference temperature (K) =
tau_t = 0.3 0.3
ref_t = 323 323
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 3.0
compressibility = 3e-5
ref_p = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 323
gen_seed = 666
; OPTIONS FOR BONDS =
; MARTINI - for ring systems constraints are defined
; which are best handled using Lincs.
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
is it because i didn't do the heating/equilibration run first?
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- djurre
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11 years 10 months ago #998
by djurre
Replied by djurre on topic area per lipid
You're using isotropic pressure coupling instead of semiisotropic. This means that the x,y and z dimensions all have to scale at the same rate. Switching to semiisotropic AND making sure the bilayer is in the XY plane, will fix this.
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