Pressure scaling and position restraints

User discussions
1

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.
define = -DVESICLE_LIPIDTAIL_R=2.00 -DPOSRES_ILA

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

; GENERATE VELOCITIES FOR STARTUP RUN:
gen_vel = yes
gen_temp = 310
gen_seed = 8620317792

refcoord_scaling = all

; MARTINI and CONSTRAINTS
; 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,
Riccardo

2

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.

3

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

4

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.
Best,
Riccardo

5

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?

6

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