Pressure scaling and position restraints

GROMACS version: 2020
GROMACS modification: Yes/No
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Dear all,
I am trying to simulate a system using Gromacs 2020 and the Martini CG force field. My system contains a micelle inserted in the middle of the box, some lipids around it and finally solvent and counterions.
The point is that when I try to equilibrate the system in the NPT ensembe, after running an EM, using position restraints I always receive back this message “Step 100 Warning: pressure scaling more than 1%, mu: 1.89195e+16 1.89195e+16 1.89195e+16”. However, if I try to run the same equilibration without applying position restraints, everything goes smooth. I am wondering if someone could give me any advice. I am also posting the mdp configuration.

integrator = md
tinit = 0.0
dt = 0.002
nsteps = 50000

nstlog = 10000
nstenergy = 10000
nstxout-compressed = 10000
compressed-x-precision = 10000

cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005

epsilon_r = 15
coulombtype = reaction-field
rcoulomb = 1.1
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1

tcoupl = v-rescale
tc-grps = POPC_ILA W_WF_ION
tau_t = 1.0 1.0
ref_t = 310 310

; Pressure coupling:
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p = 12.0
compressibility = 4.5e-5
ref_p = 1.0

;Freezen ILq in x,y,z coord
;freezegrps = ILA
;freezedim = Y Y Y

gen_vel = yes
gen_temp = 310
gen_seed = 8620317792

refcoord_scaling = all

; for ring systems and stiff bonds constraints are defined
; which are best handled using Lincs.

constraints = none
constraint_algorithm = Lincs

Thank you all in advance,

Hi - you’re doing the Martini vesicle interleaflet equilibration procedure? Try gradually scaling up the vesicle radius in a series of smaller steps, the pressure coupling is probably a red herring, and your system is exploding from the equilibration.

Ah I missed your system description in the first comment - I’m not familiar with the micelle equilibration procedure, is there a pore formation step? If not, you shouldn’t have that DVESICLE_LIPIDTAIL_R parameter

Hi Kevin,
thank you for your kind advise. I am not familiar with the Martini vescicle interleaflet equilibration, I am wondering if you could be more specific.
On the other hand, there is not a pore formation step, I will delete the DVESCICLE_LIPIDTAIL_R option.

That DVESICLE_LIPIDTAIL_R typically is associated with a cylindrical potential along all 3 axes that is repulsive to lipid tail beads. It’s used to form pores in vesicles so that lipids can move between leaflets during equilibration.

Did removing the parameter work?

yes thank you. I’ve removed that parameter and applied restraints using the -r option and now everything is going smooth.
Thank you