[gmx-users] Bilayer exploding with semiisotropic coupling

[Paul Bauer]

Hello,

please upload the log file from the run, as well as the command you used to
run the simulation and your system specs (processor, whether you are using
GPUs).

Then we can see what is wrong here.

Thanks in advance.

Cheers

Paul

On Sat, 4 Jan 2020, 21:14 Kevin Boyd, <kevin.boyd at uconn.edu> wrote:

> 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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