GROMACS version: 2016.3
GROMACS modification: No
I’ve been trying to get this CG simulation of two vesicles of 1000 lipids each in water and I’ve been having difficulty going from the minimization step to equilibration step. I was getting these errors saying pressure scaling was too high which as I learned indicates a system that isn’t fully minimized.
Messing aroung with some the equilibration mdp settings, I managed to get something running with most of the settings from the equilibration.mdp file. There wasn’t much to change, I was able to introduce the pressure scaling and changed the define line from -DFLEXIBLE, which is what it was set to in the minimization.mdp file to -DVESICLE_LIPIDTAIL_R=2.00, as it is in the default equilibration.mdp files, (there are multiple equilibration steps with this 2.00 value decreasing slowly to 0.20 but the first step uses 2.00). If you look below you can see the settings for both the files are the same with this one exception.
After having this semi-equilibration step run for 10ns, I looked through trajectory to see what happens to the two vesicles, most of the pores that come built in by charmm-gui close except for one on each. I tried continuing the equilibration from this result and ran into the same issues I did before with the pressure scaling. In fact when I looked at the trajectory of what is simulated before the it crashes, the lipids of the vesicles get pushed apart from each other losing the spherical shape, they are in groups but just not the vesicles that I’m trying to end up with. From what I think I understand, this -DFLEXIBLE has something to do with specifying the step to use flexible water model vs rigid water model(?), so removing this I presume, results in water molecules that were in an “unnatural” shape being restrained into their expected shapes, this causes a change in the equilibration state and then pushes everything apart. This is what’s happening? And if so would further minimization fix the issue? Any feedback is appreciated.
Some further notes about the simulation, the dimensions of the box are x=42nm, y=30, z = 30.
define = -DFLEXIBLE/-DVESICLE_LIPIDTAIL_R=2.00
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 5000000
nstlog = 1000
nstenergy = 1000
nstxout-compressed = 1000
compressed-x-precision = 100
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 = vesicles solute
tau_t = 1.0 1.0
ref_t = 310 310
; Pressure coupling:
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p = 5.0
compressibility = 4.5e-5
ref_p = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN:
gen_vel = yes
gen_temp = 310
gen_seed = 9118296431
refcoord_scaling = all