[gmx-users] simulation box

[Justin A. Lemkul]

Quoting sudheer babu <sudheer.pbm07 at gmail.com>:

> Hi gmx-users,
> I added simulation box by *editconf below mentioned to POPC system
> downloaded from Tieleman's website, I don't want to add water
> 1) *editconf -f popc.gro -o popc_box.gro -box 6 6 9 -c  this one I followed
> based on gmx-archives.
> 2) Then in 2ndcase I used same command but 8 8 8(cubic) instead of 1st case
> numerical values .
>  After this I did *EM system is fine for both cases when visualise in VMD.
> when I do *PR I am getting problem in second way of using *editconf rather
> than first way. I got fine structure in first case (without distortions in
> water and membrane). In 2nd case displacement of water ( totally there is no
> cubic structure at all ). Now my doubt is shall I use 1 case output file for
> my further simulations? or any mistake in my command or pr.mdp file ? while
> I am using it runs fine. Is it mandatory to add cubic box?

I don't see what you're aiming to do.  Using an 8-nm cubic box around a roughly
6-nm cubic system will essentially place the bilayer system in the middle of a
vacuum.  Undoubtedly the water is going to expand into the void.  If you were
to remove the position restraints from the lipids, I suspect they would move
erratically as well.

The 6 x 6 x 9 system will also have some vacuum above and below the bilayer
system, and water will likely expand into those regions as well, given enough
time.

-Justin

>
> Pls help me I am posting my pr.mdp file(similar parameter for both cases)
>
> title               =   popc restrained
> define              =  -DPOSRES_LIPID
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  10000    ; total 50 ps.
> nstcomm             =  1
> nstxout             =  50
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  10
> nstenergy           =  10
> nstlist             =  10
> ns_type             =  grid
> rlist               =  0.9
> coulombtype         =  PME
> rcoulomb            =  0.9
> rvdw                =  1.4
> pbc                 =  xyz
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  Berendsen
> tc-grps             =  POPC     SOL
> tau_t               =  0.1      0.1
> ref_t               =  323      323
> ; Anisotropic pressure coupling is now on
> Pcoupl              =  berendsen
> pcoupltype          =  anisotropic
> tau_p               =  1.0      1.0     1.0    1.0      1.0     1.0
> compressibility     =  4.5e-5   4.5e-5  4.5e-5  0        0       0
> ref_p               =  1.0      1.0     1.0     0        0       0
> ; Energy monitoring
> energygrps          =  POPC     SOL
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  323.0
> gen_seed            =  173529
> ~
> Thanks in advance.
>



========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================