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NVE ensemble with Martini lipid
- jmondal
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10 years 5 months ago #351
by jmondal
NVE ensemble with Martini lipid was created by jmondal
Hi,
I am having a problem with running a NVE ( micro-canonical) ensemble using a system of 128 Martini DPPC lipids. I started the simulation with a 128 lipid bilayer with Martini water which was pre-equilibrated in NPT ensemble ( using berendsen temperature coupling at 325 K( separate coupling for lipid and water) and pressure coupling at 1 atm for 500 ns).
But, when I started running the NVE simulation by switching off pressure coupling and temperature coupling, the temperature started going down from 325 to almost 2 K very quickly which looks like very unphysical. However, total energy remains conserved . But the temperature is becoming a concern as it is going down to a 0 K. I am not sure whether I am doing some mistake in the mdp parameter. Any help will be appreciated.
Here is the part of mdp option I used for running with gromacs-4.0.7
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0.0
dt = 0.020
nsteps = 25000000
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files separate)
simulation_part = 1
init_step = 0
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps = DPPC Nonlipid
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 10
emstep = 0.01
; Max number of iterations in relax_shells
niter = 20
; Step size (ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; TEST PARTICLE INSERTION OPTIONS
rtpi = 0.05
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 500
nstvout = 500
nstfout = 0
; Output frequency for energies to log file and energy file
nstlog = 500
nstenergy = 500
; Output frequency and precision for xtc file
nstxtcout = 500
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 Nonlipid
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 10
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic_molecules = no
; nblist cut-off
rlist = 1.4
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Relative dielectric constant for the medium and the reaction field
epsilon_r = 15
epsilon_rf = 1
; 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
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Seperate tables between energy group pairs
energygrp_table =
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
; Temperature coupling
tcoupl = no
; Groups to couple separately
tc-grps =
; Time constant (ps) and reference temperature (K)
tau-t =
ref-t =
; Pressure coupling
Pcoupl = no
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p = 1
compressibility =
ref-p =
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = No
; Random seed for Andersen thermostat
andersen_seed = 815131
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 325
gen_seed = 473529
; OPTIONS FOR BONDS
constraints = none
; Type of constraint algorithm
constraint_algorithm = Lincs
; Do not constrain the start configuration
continuation = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 0.0001
; Highest order in the expansion of the constraint coupling matrix
lincs_order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs_warnangle = 30
; Convert harmonic bonds to morse potentials
morse = no
Thanks
Sanku
I am having a problem with running a NVE ( micro-canonical) ensemble using a system of 128 Martini DPPC lipids. I started the simulation with a 128 lipid bilayer with Martini water which was pre-equilibrated in NPT ensemble ( using berendsen temperature coupling at 325 K( separate coupling for lipid and water) and pressure coupling at 1 atm for 500 ns).
But, when I started running the NVE simulation by switching off pressure coupling and temperature coupling, the temperature started going down from 325 to almost 2 K very quickly which looks like very unphysical. However, total energy remains conserved . But the temperature is becoming a concern as it is going down to a 0 K. I am not sure whether I am doing some mistake in the mdp parameter. Any help will be appreciated.
Here is the part of mdp option I used for running with gromacs-4.0.7
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0.0
dt = 0.020
nsteps = 25000000
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files separate)
simulation_part = 1
init_step = 0
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps = DPPC Nonlipid
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 10
emstep = 0.01
; Max number of iterations in relax_shells
niter = 20
; Step size (ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; TEST PARTICLE INSERTION OPTIONS
rtpi = 0.05
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 500
nstvout = 500
nstfout = 0
; Output frequency for energies to log file and energy file
nstlog = 500
nstenergy = 500
; Output frequency and precision for xtc file
nstxtcout = 500
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 Nonlipid
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 10
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic_molecules = no
; nblist cut-off
rlist = 1.4
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Relative dielectric constant for the medium and the reaction field
epsilon_r = 15
epsilon_rf = 1
; 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
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Seperate tables between energy group pairs
energygrp_table =
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
; Temperature coupling
tcoupl = no
; Groups to couple separately
tc-grps =
; Time constant (ps) and reference temperature (K)
tau-t =
ref-t =
; Pressure coupling
Pcoupl = no
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p = 1
compressibility =
ref-p =
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = No
; Random seed for Andersen thermostat
andersen_seed = 815131
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 325
gen_seed = 473529
; OPTIONS FOR BONDS
constraints = none
; Type of constraint algorithm
constraint_algorithm = Lincs
; Do not constrain the start configuration
continuation = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 0.0001
; Highest order in the expansion of the constraint coupling matrix
lincs_order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs_warnangle = 30
; Convert harmonic bonds to morse potentials
morse = no
Thanks
Sanku
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- andrzej
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- Posts: 34
10 years 5 months ago #361
by andrzej
Replied by andrzej on topic NVE ensemble with Martini lipid
Hey
I think reading will clear Your questions.
S.J. Marrink, X. Periole, D.P. Tieleman, A.H. de Vries. Comment on using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models. Phys. Chem. Chem. Phys., 12:2254-2256, 2010.
Andrzej
I think reading will clear Your questions.
S.J. Marrink, X. Periole, D.P. Tieleman, A.H. de Vries. Comment on using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models. Phys. Chem. Chem. Phys., 12:2254-2256, 2010.
Andrzej
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