[gmx-users] simulation box
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 27 20:40:25 CET 2008
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
> 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
jalemkul at vt.edu | (540) 231-9080
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