[gmx-users] Bilayer exploding with semiisotropic coupling

[Kevin Boyd]

Hi,

Can you share more information? Please upload your starting configuration
and a log file.

On Fri, Jan 3, 2020 at 10:29 AM Namit Chaudhary <nchaudha at andrew.cmu.edu>
wrote:

> Hi,
>
> Sorry. I didn't realize that attachments aren't uploaded. Below is a link
> for the files mentioned in the original mail.
>
> https://drive.google.com/drive/folders/1fUrx4yt3DpCEGY0CACA6n-PXcswfaa31?usp=sharing
>
> Namit
>
> On Fri, Jan 3, 2020 at 1:12 PM Namit Chaudhary <nchaudha at andrew.cmu.edu>
> wrote:
>
> > 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
> >
>
>
> --
> *Namit Chaudhary*
> Chemical Engineering | Carnegie Mellon University
> M: 724-506-0693 | E: nchaudha at andrew.cmu.edu
> --
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