[gmx-users] simulation box
sudheer.pbm07 at gmail.com
Wed Feb 27 20:07:00 CET 2008
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.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users