unanswered CG protein escaping from CG lipid monolayer

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8 months 2 weeks ago #7709 by Imamul
Hi all,
I am trying to simulate a CG system consists of DPPC, POPG, CHOL and SP-B (1-25). The system also consists 21nm CG water_ION separated by two lipids_protein (DPPC_POPG_CHOL_SP-B) monolayers ( www.dropbox.com/s/tdd5odmadgfqrm5/2.JPG?dl=0 ). Each monolayer having 657 DPPC, 279 POPG, 90 CHOL and 9 SP-B. The proteins were inserted using INSANE script. I minimized this system properly before going to 200ns equilibration at 20fs time step using surface tension coupling. During the equilibration I restrained the position of the proteins. After equilibration, I went for production run for 3 microsecond without restraint the position of the protein. The problem occured after 200ns production run, one protein expelled ( www.dropbox.com/s/bbftlbcfw0mzsxh/4.JPG?dl=0 ) from the monolayer and remained in the water. But after 3 microsecond, this protein attached with the bilayer reservoir connected to the monolayer. The bilayer reservoir formed after buckling and folding of the monolayer with a drastic change in lateral dimension from 25nm to 15.4nm. As a result the water thickness increased significantly ( www.dropbox.com/s/3mktui3a34iosyz/Simula..._after_3_us.png?dl=0 ).

I am not sure why the protein spelled out from the monolayer during simulation.

N.B. For better visualization I removed water and ION in some of the above figures.

The following mdp file was used in the production run

; VARIOUS PREPROCESSING OPTIONS =
title = Martini
cpp = /usr/bin/cpp

; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
dt = 0.02
nsteps = 150000000
; number of steps for center of mass motion removal =
nstcomm = 100
comm-grps = System
comm-mode = linear

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
;nstxout = 5000
;nstvout = 5000
;nstfout = 5000
; Output frequency for energies to log file and energy file =
nstlog = 5000
nstenergy = 100
nstcalcenergy = 100
; 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 = DPPC_POPG_CHOL W_ION Protein

; NEIGHBORSEARCHING PARAMETERS =
cutoff-scheme = Verlet
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or none =
pbc = xyz
verlet-buffer-tolerance = 0.005
rlist = 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = cutoff
coulomb-modifier = Potential-shift
rcoulomb = 1.2
rcoulomb-switch = 0
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 15
; Method for doing Van der Waals =
vdw_type = cutoff
vdw-modifier = Potential-shift
rvdw = 1.2
rvdw-switch = 0.9
epsilon_rf = 0

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = V-rescale
nsttcouple = 2
; Groups to couple separately =
tc-grps = DPPC_POPG_CHOL W_ION Protein
; Time constant (ps) and reference temperature (K) =
tau_t = 1.0 1.0 1.0
ref_t = 310 310 310
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = surface-tension
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 4
compressibility = 4.5e-5 0
ref_p = 0 1.0

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 310
gen_seed = -1


; 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

Regards
Imamul

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