fix wall/reflect time integration

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1

Hello,

I’m trying to squeeze my molecule in simulation box and see the effect of pressure by moving walls. I use wall/reflect and NVT for time integration. but I don’t see signeficant pressure change in the course of run. Niether I see any moving in boundary walls in VMD. is it because of NVT setting? is there another time integration to use with “fix wall/reflect”?

here is the input file that I use:

units lj
dimension 3
boundary f f f
atom_style angle

read_data data_long.dat
read_dump dump.md 1020000 x y z
velocity all create 0.1 23656 dist gaussian

bond_style harmonic
bond_coeff 1 1 1.2

pair_style lj/cut 10
pair_coeff 1 1 0.2 1.0
pair_modify shift yes
pair_coeff 1 2 1.0 1.0 1.122
pair_coeff 2 2 1.0 1.0 1.122

neigh_modify page 30000
neigh_modify one 3000

angle_style harmonic
angle_coeff 1 10 180
angle_coeff 2 0.0 180

fix 1 all nvt temp 0.1 0.1 0.1
lattice fcc 0.003
variable ramplo equal ramp(-50,-0.0002)
variable ramphi equal ramp(50,0.0002)
fix walls all wall/reflect xlo v_ramplo xhi v_ramphi ylo v_ramplo yhi v_ramphi zlo v_ramplo zhi v_ramphi

thermo 2000
dump 1 all custom 3000 ext_chain_long_bnd_no_interaction_wall.md id type xu yu zu
timestep 0.000005
run 100000

Best,

Hamed.

2

units lj
…
lattice fcc 0.003
variable ramplo equal ramp(-50,-0.0002)
variable ramphi equal ramp(50,0.0002)
fix walls all wall/reflect xlo v_ramplo xhi v_ramphi ylo v_ramplo yhi v_ramphi zlo v_ramplo zhi v_ramphi

From the wall/reflect doc page:
In the variable case, the variable is assumed to produce a value compatible with the units setting you specify.

You specify lattice with 0.003, and the default units is lattice, not box. So unless you
have thought carefully about it, the wall is likely not where you expect it to be.
A lattice setting of 0.003 for LJ units means the lattice spacing
is humongous, since 0.003 is a density.

I suggest you try units box and no lattice command and have your variable
return a position in box coordinates, so you can verify it is where you expect
it to be.

Steve