[gmx-users] Bilayer exploding with semiisotropic coupling

[Namit Chaudhary]

Hi all,

I am trying to simulate a coarse grain system containing DPPC (10%),
Cholesterol (40%) and a custom lipid that's synthesized by our lab (50%,
topology and martini mapping attached).  Our lab uses these molecules to
formulate lipid nanoparticles and deliver RNA therapeutics. I am trying to
understand the structure of these nanoparticles. I tried modelling them as
a bilayer but the system seems to be exploding in the z - direction during
the production run if I use semiisotropic or anisotropic pressure coupling
(isotropic coupling seems to work).  Below is the md.mdp file that I am
using.

integrator               = md
dt                           = 0.01
nsteps                   = 8000000
nstcomm               = 100
comm-grps            = LIPIDS SOL


nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
nstlog                   = 1000  ; Output frequency for energies to log
file
nstenergy                = 100   ; Output frequency for energies to energy
file
nstxtcout                = 1000  ; Output frequency for .xtc file
xtc_precision            = 100
xtc-grps                 =
energygrps               =


nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.1

coulombtype              = reaction_field  ;Reaction_field (for use with
Verlet-pairlist) ;PME (especially with polarizable water)
rcoulomb_switch          = 0.0
rcoulomb                 = 1.1
epsilon_r                = 15 ; 2.5 (with polarizable water)
vdw_type                 = cutoff  ;cutoff (for use with Verlet-pairlist)
rvdw_switch              = 0.9
rvdw                     = 1.1 ;1.1 (for use with Verlet-pairlist)

cutoff-scheme            = verlet

tcoupl                   = v-rescale
tc-grps                  = LIPIDS SOL
tau_t                     = 1.0  1.0
ref_t                      = 298 298
Pcoupl                   = parrinello-rahman
Pcoupltype            = semiisotropic
tau_p                     = 12.0
compressibility       = 3e-4 3e-4      ; 3e-4
ref_p                      = 1.0 1.0       ; 1.0 1.0

gen_vel                    = yes
gen_temp                 = 298
gen_seed                 = 473529

constraints                = none
constraint_algorithm = Lincs
continuation              = no
lincs_order                = 4
lincs_warnangle        = 30

Is there something that I can change in my mdp file? Or is there something
wrong with the lipid itself?


Thank you
Namit