[gmx-users] Equilibration step not moving forward

[Kevin Boyd]

Hi,

We can't help you unless you're more specific. What error is occurring?

Kevin

On Tue, Feb 5, 2019 at 1:30 AM Deepanshi <sdeepanshi293 at gmail.com> wrote:

> 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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