[gmx-users] how to create a decane slab!!

[nanyu101]

Dear gmx-users,

   I have tried to simulate an ion channel inserting into the bilayer.Can I simulate the ion channel inserting into the DPPC given by Dr.Tieleman?
   
    I want to simulate the ion channel how to insert into the decane slab or actane slab firstly.The decane gro and itp files are in the top directory,so i think it is easier to create a decane slab.Should I use these files to create an octane slab?

   But now,I am trouble in minimizing the decane slab. My mdp file is listed as following:
title               =  try decane
cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  steep
nsteps              =  200000
nslist              =  5
ns_type             =  grid
pbc                 =  xyz
rlist               =  0.9
coulombtype         =  PME
rcoulomb            =  0.9
rvdw                =  1.1
fourierspacing      =  0.12
fourier_x           =  0
fourier_y           =  0
fourier_z           =  0
pme_order           =  4
ewald_rtol          =  1e-5
optimize_fft        =  yes
emtol               =  500
emstep              =  0.001
Tcoupl              =  no
pcoupl              =  no
gen_vel             =  no


  I do know the PME type is no needed because the decane slab has no charge. But i can't minimized thie bilayer.In this system,the SPC waters are added  in the z direction.

   If I have tried to added the SPC water in three directions,the minimization is very easy. So,the result was used to run dynamics with following conditions:
title               =  try decane
cpp                 =  /lib/cpp
define              = -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002
nsteps              =  450000
nslist              =  10
nstxout             =  500
nstlog              =  500
nstenergy           =  500
nstxtcout           =  100
ns_type             =  grid
pbc                 =  xyz
rlist               =  0.9
coulombtype         =  pme
rcoulomb            =  0.9
rvdw                =  1.2
fourierspacing      =  0.12
pme_order           =  4
ewald_rtol          =  1e-5
optimize_fft        =  yes
Tcoupl              =  berendsen
tau_t               =  0.1  0.1
tc-grps             =  C10  SOL
ref_t               =  300  300
pcoupl              =  berendsen
pcoupltype          =  anisotropic
tau_p               =  1.0 1.0 1.0 0 0 0
compressibility     =  4.5e-5 4.5e-5 4.5e-5 0 0 0
ref_p               =  1.0 1.0 1.0 0 0 0
E_z                 =  1 2.5 0
gen_vel             =  yes
gen_temp            =  300
gen_seed            =  11


 After the MD results, the decane slab is in the center,the waters stayed in the x and y directions,there is no any water in the z direction. So would you please give me some advices?Thanks a lot.

Any comments are appreciated!!!!!!!!

Best wishes,
Xianhui Wu 
______________________________________
Best wishes,
nanyu
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