[gmx-users] simulation box

[sudheer babu]

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?

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.
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