[gmx-users] Bilayer exploding with semiisotropic coupling

[Namit Chaudhary]

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