Hi everyone,
I am trying to simulate a polymer in a water box with Martini force field, and
with a constant thickness. To realize this, I am testing simulations with wall
potential. My mdp file is as following:
integrator = md
dt = 0.002
nsteps = 500000
nstcomm = 10
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 5000
nstxtcout = 5000
xtc_precision = 100
xtc-grps =
energygrps = Sol W
cutoff-scheme = group
nstlist = 10
ns_type = grid
pbc = xy
periodic-molecules = no
rlist = 1.4
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
;walls
nwall = 2
wall-atomtype = P5 P5 ;P5 is a Martini particle type
wall-type = 10-4
wall-r-linpot = 1 1
wall-density = 1.2 1.2
wall-ewald-zfac = 3
tcoupl = berendsen
tc-grps = Sytem ;W
tau_t = 1.0 ;1.0
ref_t = 310 ;310
pcoupl = no ; no pressure coupling in NVT
gen_vel = yes
gen_temp = 310
gen_seed = -1
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
The system box was 7.0 by 7.0 by 7.0 nm, was placed at zero point by editconf
initially. Here is the head of my system:
1GLF B4 1 4.487 3.844 3.538
1GLF B5 2 4.360 4.133 3.770
1GLF B6 3 4.286 3.687 3.477
2GLF B1 4 4.409 4.396 3.647
2GLF B2 5 4.119 4.561 3.704
2GLF B3 6 4.533 4.499 3.435
2GLF B4 7 4.022 4.860 3.578
2GLF B5 8 3.961 4.977 3.209
But soon as the simulations started, some water molecules moved across the
walls, and far away in Z direction. The main box was moved in Z direction as
well:
1GLF B4 1 3.175 4.176-309.166 0.0008 0.0012 -0.3582
1GLF B5 2 3.082 4.558-309.239 0.0010 -0.0008 -0.3564
1GLF B6 3 3.188 3.981-309.342 -0.0042 0.0017 -0.3578
2GLF B1 4 2.936 4.683-309.448 0.0004 -0.0040 -0.3567
2GLF B2 5 2.602 4.708-309.427 0.0010 0.0007 -0.3586
2GLF B3 6 2.990 4.709-309.710 0.0004 0.0001 -0.3614
2GLF B4 7 2.375 4.788-309.664 0.0026 -0.0004 -0.3591
2GLF B5 8 2.150 4.640-309.969 -0.0006 -0.0007 -0.3620
As I used NVT ensemble, the box size shown in the gro file was still 7.0 by 7.0
by 7.0 nm. But I am sure in this case how the wall potential was applied. Where
is the two walls? Are they still at z=0 and box_z?
Could anyone help to check if there are anything wrong in my input files? I
have tried to change wall-atomtype, wall-type, wall-r-linpot, and wall-density,
with higher wall-density (such as 12), the box was separated into parts with a
huge z range (see the following figure). The figure is hard to see, the light
blue "particles" you could see are my system.
[cid:[email protected]]
Thanks very much.
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