normal Martini maker vesicle pores enlarge during equilibration

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2 years 5 months ago #9285 by rptang
Hi all,

I have been partially following the Martini Vesicle Maker tutorial (under Martini 2 tutorials > Others > CHARMM-GUI Martini Maker). With the Vesicle Maker program, I used these settings: vesicle only system, martini22 (not dry), vesicle radius 150 angstroms, water pore radius 5 angstroms, and only DPPC (1:1 leaflet ratio).

Due to some errors with the solvated files that were generated, I instead solvated the vesicle with the Martini waterbox water.gro provided in a different tutorial. I ran the minimization as provided until convergence (the Fmax was still around 1e2), but when I try to run the equilibration, I found that the water pores become larger and larger, so I've paused the equilibration to try to fix this issue.

Does anyone know what might be causing the pores to enlarge, and what I may do to fix it?

Thank you.

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The commands I used:
gmx editconf -f 150A_dry.pdb -o 150A_box.pdb -c -d 4.0 -bt cubic ;made the box
gmx solvate -cp 150A_box.pdb -cs water.gro -o 150A_solvated.gro ;solvated and converted to .gro
gmx grompp -f minimization1.mdp -c 150A_solvated.gro -p system.top -o 150A_minimization1.tpr
gmx genion -s 150A_minimization1.tpr -o 150A.gro -p system.top -pname NA -nname CL -neutral -conc 0.15 ;add ions
gmx make_ndx -f 150A.gro -o index.ndx ;modify .ndx to have "membrane" and "solute" groups
gmx grompp -f minimization1.mdp -c 150A.gro -p system.top -o 150A_minimization1.tpr -r lipidtail_posres.pdb -n index.ndx
gmx mdrun -deffnm 150A_minimization1 -v -c 150A_minimization1.gro ;start minimization 1
gmx grompp -f minimization2.mdp -c 150A_minimization1.gro -p system.top -o 150A_minimization2.tpr -r lipidtail_posres.pdb -n index.ndx
gmx mdrun -deffnm 150A_minimization2 -v -c 150A_minimization2.gro ;start minimization 2
gmx grompp -f equilibration1.mdp -o 150A_equilibration1.tpr -c 150A_minimization2.gro -p system.top -r lipidtail_posres.pdb -n index.ndx
gmx_mpi mdrun -deffnm 150A_equilibration1 -v ;start equilibration 1

My .mdp files:
Minimization 1 (soft-core potentials):
define = -DFLEXIBLE
integrator = steep
tinit = 0.0
nsteps = 5000

nstlog = 100
nstenergy = 100
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 = membrane solute
tau_t = 1.0 1.0
ref_t = 303.15 303.15

; 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 = 303.15
gen_seed = 4182793106

;soft-core-minimization so that single precision GROMACS works here
; Free energy parameters
free-energy = yes
init-lambda = 0.01
sc-alpha = 4
sc-power = 2
sc-coul = yes
nstdhdl = 0
couple-moltype = system
; we are changing both the vdw and the charge. In the initial state, both are on
couple-lambda0 = vdw-q
; in the final state, both are off.
couple-lambda1 = none
couple-intramol = yes

refcoord_scaling = all

Minimization 2:
define = -DFLEXIBLE
integrator = steep
tinit = 0.0
nsteps = 500000

nstlog = 100
nstenergy = 100
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 = membrane solute
tau_t = 1.0 1.0
ref_t = 303.15 303.15

; 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 = 303.15
gen_seed = 4182793106

refcoord_scaling = all

Equilibration 1:
define = -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 = membrane solute
tau_t = 1.0 1.0
ref_t = 303.15 303.15

; 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 = 303.15
gen_seed = 4182793106

refcoord_scaling = all

My .top file:
#include "toppar/martini_v2.2.itp"
#include "toppar/martini_v2.0_lipids_all_201506.itp"
#include "toppar/martini_v2.0_ions.itp"

[ system ]
; name
Martini system

[ molecules ]
; name number
DPPC 91872
W 503739
NA 5666
CL 5666

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2 years 5 months ago #9286 by bart
Hard to say, do they restore? One thing could be your water is freezing (Martini2 without antifreeze).

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2 years 5 months ago #9288 by rptang
Thank you for your message, bart. The equilibration so far has shown the pore radius increasing at a seemingly constant rate without slowing down, but I've only run around 100ns so far. Maybe they will restore after 1us, but this was unexpected since the vesicle tutorials do not indicate that they would enlarge before shrinking again.

What is the best method to tell if the water is frozen? As far as I can tell visually, all of the water beads seem to be moving the entire time.

I can try out the longer simulation and antifreeze water. Thanks!

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2 years 5 months ago #9289 by bart
100 ns is already a long time for pressure equilibratiin through the pore.

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