Thomas Schmidt wrote:
Dear all,
by doing MD simulations of a protein complex embedded in 2 membranes
(inner and outer membrane of bacteria, POPE), we observe a bilayer
splitting in one of the membranes. This has the effect that the bilayer
forms "bubbles" with vacuum inside.
We have seen this before with POPE membranes, which appear to be particularly
problematic. We solved it by using a better equilibration protocol that
involved simulated annealing (from a very low temperature up to 310 K). For us,
it seemed to happen independently of just about anything we tried.
-Justin
It might have something to do with the PME handling of GroMACS 4.0.3
(GROMOS96-53a6 ff).
- there is no splitting using a 1 nm smaller boxsize in exactly the same
model
- if we switch off the PME mode and use only Cut-off's we don't have
any splitting effect
- the behavior of the bilayer splitting depends on the number of used
cluster/cpu nodes
Changing the "fourierspacing" parameter to create different PME grids
has no effect to avoid bilayer splitting.
Changing: thermostat | barostat (semiisotropic):
- berendsen | berendsen: "splitting"
- v-rescale | parrinello-rahman: "splitting"/"keep together" (50:50)
Here's the mdp file of our last try:
title = Yep, sometimes I will cause a bilayer splitting;
; The following lines tell the program the standard locations where to
find certain files
cpp = cpp; Preprocessor
include = -I../top; Directories to include in the topology
format
define = -DPOSRES; Apply position restraints.
; RUN CONTROL PARAMETERS
integrator = MD
; Start time and timestep in ps
tinit = 0
dt = 0.002
nsteps = 10000000
; For exact run continuation or redoing part of a run
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 = Protein POPE_center POPE_inner POPE_outer
SOL_NA+_CL-
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 500
emstep = 0.01
; Max number of iterations in relax_shells
niter = 0
; Step size (1/ps^2) for minimization of flexible constraints
fcstep = 0
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 500000
nstvout = 500000
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 50000
; Output frequency for energies to log file and energy file
nstlog = 5000
nstenergy = 5000
; Output frequency and precision for xtc file
nstxtcout = 50000
xtc-precision = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps = Protein POPE_center POPE_inner POPE_outer
SOL_NA+_CL-
; Selection of energy groups
energygrps = Protein POPE_center POPE_inner POPE_outer
SOL_NA+_CL-
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 10
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 1.15
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.15
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 1.4
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; 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 = yes
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
; Tcoupl = berendsen
Tcoupl = V-rescale
; Groups to couple separately
tc-grps = Protein POPE_center POPE_inner POPE_outer
SOL_NA+_CL-
; Time constant (ps) and reference temperature (K)
tau-t = 0.1 0.1 0.1 0.1 0.1
ref-t = 310 310 310 310 310
; Pressure coupling
; Pcoupl = berendsen
Pcoupl = Parrinello-Rahman
Pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p = 4 4
compressibility = 4.5e-5 4.5e-5
ref-p = 1.0 1.0
; Random seed for Andersen thermostat
andersen_seed = 815131
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen-temp = 310
gen-seed = 24071998
; OPTIONS FOR BONDS
constraints = all-bonds
; Type of constraint algorithm
constraint-algorithm = Lincs
; Do not constrain the start configuration
unconstrained-start = yes
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 1e-04
; 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 = 4
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 90
; Convert harmonic bonds to morse potentials
morse = no
Does anyone have any idea?
Many thanks for your time and any help.
Cheers,
Thomas
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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