GROMACS version: 2020.4
GROMACS modification: No
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Dear GROMACS users,
I am trying to perform all-atom lipid self-assembly into bilayers. My idea is to set a the initial conditions using pure POPC add an amphiphilic molecule and see the effect in the bilayer formation.
I am currently using Lipids21, TIP3P, and potassium ff99 counterions, similarly to this article: Simulation of lipid bilayer self-assembly using all-atom lipid force fields - Physical Chemistry Chemical Physics (RSC Publishing)
Hower, I am having some trouble. In some cases, after the initial aggregation of the molecules, there is somtimes a short step of bilayer formation, and then one of the axis gets extremely elongated, so molecules are dispered in a way that they are interacting with themselves in the periodic boxes. As images show:
This has happened several times, with different initial configurations. I have no idea how solve this.
Is anyone familiar with self-assembly simulations that has encountered this issue before?
Here I leave my production run .mdp (equilibration is run in isotropic conditions, so no distorsion is seen).
Thanks a lot for your time and help!
title = NPT production
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 250000000 ; 2 * 250000000 = 500000000 ps (500 ns)
dt = 0.002 ; 2 fs
; Output control
nstxout = 0 ; suppress bulky .trr file by specifying
nstvout = 0 ; 0 for output frequency of nstxout,
nstfout = 0 ; nstvout, and nstfout
nstenergy = 50000 ; save energies every 100.0 ps
nstlog = 50000 ; update log file every 100.0 ps
nstxout-compressed = 50000 ; save compressed coordinates every 100.0 ps
compressed-x-grps = System ; save the whole system
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = molecules solvent ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 323 323 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = anisotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 1.0 1.0 0.0 0.0 0.0 ; reference pressure, in bar
compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off