[gmx-users] Equilibration step not moving forward

Deepanshi sdeepanshi293 at gmail.com
Tue Feb 5 07:30:14 CET 2019


Hello,
I am trying to equilibrate a bilayer vesicle which I have prepared using
martini maker of charmm-GUI. The vesicle is made up of POPC and has around
3000 lipids. I am trying to equilibrate the system but steps are not
moving forward and I am stuck at this point. Here are the details of the
.mdp file which I am using for this step:
define                   = -DVESICLE_LIPIDTAIL_R=2.00
integrator               = sd
tinit                    = 0.0
dt                       = 0.010
nsteps                   = 1000000

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

tc-grps                  = system
tau_t                    = 4.0
ref_t                    = 310

; Pressure coupling:
Pcoupl                   = no

; GENERATE VELOCITIES FOR STARTUP RUN:
gen_vel                  = yes
gen_temp                 = 310
gen_seed                 = 1549004057

refcoord_scaling         = all

Thank you.

Best Regards.
Zara.


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