[gmx-users] problem with NVE ensemble simulation with Martini lipid

[Sanku M]

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


      
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