Dear LAMMPS Users,

I have a system containing a water layer and a membrane film (system is created using Packmol). The water is initially set 10 Anstrong apart from the membrane. I want to move the water toward and eventually penetrate the membrane and observe the water-membrane interactions at each moving steps. To move the water I’m using “displace_atoms” command (please see the input description below). My question is that how do I know/calculate how fast the water moves or the water velocity?

In addition, I’m wondering if my approach is appropriate to study membrane-water interactions and would you mind letting me know better approaches. I’m currently learning MDS and really appreciate your helps.

Thank you.

Kind regards.

Vu Bui

Input file:

# initialization

units real

atom_style full

dimension 3

boundary p p p

# Atom definition

read_data Data.lmpdat

group Mem id <= 5900

group Water id > 5900

neighbor 0.3 bin

neigh_modify every 10 page 100000 one 10000

# Bond

bond_style harmonic

bond_coeff 1 350 1.53 # C:C

bond_coeff 2 350 1.09 # C:H

bond_coeff 3 350 1.371 # F:C

bond_coeff 4 350 1.462 # N:C

bond_coeff 5 350 1.022 # N:H

bond_coeff 6 350 1.42 # O:C

bond_coeff 7 350 0.98 # O:H

bond_coeff 8 350 1.96 # Ti:O

# Angle

angle_style cosine/squared

angle_coeff 1 56.25 109.471 # C: C: C

angle_coeff 2 56.25 109.471 # C: C: H

angle_coeff 3 54.5 106.7 # C: N: C

angle_coeff 4 54.5 106.7 # C: N: H

angle_coeff 5 53.35 104.51 # C: O: C

angle_coeff 6 53.35 104.51 # C: O: H

angle_coeff 7 56.25 109.471 # F: C: C

angle_coeff 8 56.25 109.471 # F: C: F

angle_coeff 9 56.25 109.471 # F: C: H

angle_coeff 10 56.25 109.471 # H: C: H

angle_coeff 11 53.35 104.51 # H: O: H

angle_coeff 12 56.25 109.471 # N: C: C

angle_coeff 13 56.25 109.471 # N: C: H

angle_coeff 14 56.25 109.471 # O: C: C

angle_coeff 15 56.25 109.471 # O: C: H

angle_coeff 16 56.25 109.471 # O: C: O

angle_coeff 17 50 90 # O: Ti: O

angle_coeff 18 53.35 104.51 # Ti: O: C

angle_coeff 19 53.35 104.51 # Ti: O: H

# Dihedrals

dihedral_style harmonic

dihedral_coeff 1 1 1 3

dihedral_coeff 2 1 1 3

dihedral_coeff 3 1 1 3

dihedral_coeff 4 1 1 3

dihedral_coeff 5 1 1 3

dihedral_coeff 6 1 1 3

dihedral_coeff 7 1 1 3

dihedral_coeff 8 1 1 3

dihedral_coeff 9 1 1 3

dihedral_coeff 11 1 1 3

dihedral_coeff 10 1 1 3

dihedral_coeff 11 1 1 3

dihedral_coeff 12 1 1 3

dihedral_coeff 13 1 1 3

dihedral_coeff 14 1 1 3

dihedral_coeff 15 1 1 3

dihedral_coeff 16 1 1 3

dihedral_coeff 17 1 1 3

dihedral_coeff 18 1 1 3

dihedral_coeff 19 1 1 3

dihedral_coeff 20 1 1 3

dihedral_coeff 21 1 1 3

dihedral_coeff 22 1 1 3

dihedral_coeff 23 1 1 3

dihedral_coeff 24 1 1 3

dihedral_coeff 25 1 1 3

dihedral_coeff 26 1 1 3

dihedral_coeff 27 1 1 3

dihedral_coeff 28 1 1 3

dihedral_coeff 29 1 1 3

dihedral_coeff 30 1 1 3

dihedral_coeff 31 1 1 3

# Pairwise

#1 12.0107 # C

#2 18.9984 # F

#3 1.00794 # H

#4 14.0067 # N

#5 15.9994 # O

#6 47.867 # Ti

pair_style hybrid/overlay lj/cut/coul/cut 10 hbond/dreiding/lj 4 2.2 3.5 90

pair_coeff 1 1 lj/cut/coul/cut 0.0238 3.473 #C

pair_coeff 2 2 lj/cut/coul/cut 0.0181 3.093 #F

pair_coeff 3 3 lj/cut/coul/cut 0.0038 2.846 #H

pair_coeff 4 4 lj/cut/coul/cut 0.0194 3.263 #N

pair_coeff 5 5 lj/cut/coul/cut 0.0239 3.033 #O

pair_coeff 6 6 lj/cut/coul/cut 0.0138 4.045 #Ti

pair_coeff 1 2 lj/cut/coul/cut 0.0208 3.283

pair_coeff 1 3 lj/cut/coul/cut 0.0095 3.160

pair_coeff 1 4 lj/cut/coul/cut 0.0214 3.368

pair_coeff 1 5 lj/cut/coul/cut 0.0238 3.253

pair_coeff 1 6 lj/cut/coul/cut 0.0181 3.759

pair_coeff 2 3 lj/cut/coul/cut 0.0083 2.970

pair_coeff 2 4 lj/cut/coul/cut 0.0187 3.178

pair_coeff 2 5 lj/cut/coul/cut 0.0208 3.063

pair_coeff 2 6 lj/cut/coul/cut 0.0158 3.569

pair_coeff 3 4 lj/cut/coul/cut 0.0086 3.055

pair_coeff 3 5 lj/cut/coul/cut 0.0095 2.940

pair_coeff 3 6 lj/cut/coul/cut 0.0072 3.446

pair_coeff 4 5 lj/cut/coul/cut 0.0215 3.148

pair_coeff 4 6 lj/cut/coul/cut 0.0163 3.654

pair_coeff 5 6 lj/cut/coul/cut 0.0181 3.539

pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 2.2 3.5 90

pair_coeff 1 4 hbond/dreiding/lj 3 i 9.5 2.75 4 2.2 3.5 90

pair_coeff 1 5 hbond/dreiding/lj 3 i 9.5 2.75 4 2.2 3.5 90

pair_coeff 2 4 hbond/dreiding/lj 3 j 9.5 2.75 4 2.2 3.5 90

pair_coeff 2 5 hbond/dreiding/lj 3 j 9.5 2.75 4 2.2 3.5 90

pair_coeff 4 5 hbond/dreiding/lj 3 j 9.5 2.75 4 2.2 3.5 90

pair_coeff 5 5 hbond/dreiding/lj 3 j 9.5 2.75 4 2.2 3.5 90

#output

thermo 1000

velocity all create 298.0 51515

fix 1 all nve

fix 2 all langevin 298 298 0.01 904297

fix 3 all temp/rescale 1 298 298 0.01 1 units box

compute hb all pair hbond/dreiding/lj

variable n_hbond equal c_hb[1] #number hbonds

variable E_hbond equal c_hb[2] #hbond energy

thermo_style custom step temp density etotal pe ke emol evdwl ecoul v_E_hbond v_n_hbond epair ebond eangle edihed enthalpy elong etail

timestep 0.001

dump 1 all xyz 10000 dM.xyz

dump 2 all image 10000 pM.*.jpg type type

# Run a Simulation

run 10000

unfix 1

unfix 2

unfix 3

fix 1 all nve

fix 2 all langevin 298 298 0.01 904297

fix 3 all temp/rescale 1 298 298 0.01 1 units box

displace_atoms Water move 0 0 -5 units box

dump 3 all xyz 10000 dM2.xyz

dump 4 all image 10000 pMw2.*.jpg type type

run 10000

unfix 1

unfix 2

unfix 3

fix 1 all nve

fix 2 all langevin 298 298 0.01 904297

fix 3 all temp/rescale 1 298 298 0.01 1 units box

displace_atoms Water move 0 0 -5 units box

dump 5 all xyz 10000 dM3.xyz

dump 6 all image 10000 pM3.*.jpg type type

run 10000

unfix 1

unfix 2

unfix 3

fix 1 all nve

fix 2 all langevin 298 298 0.01 904297

fix 3 all temp/rescale 1 298 298 0.01 1 units box

displace_atoms Water move 0 0 -2 units box

dump 7 all xyz 10000 dM4.xyz

dump 8 all image 10000 pM4.*.jpg type type

run 10000

unfix 1

unfix 2

unfix 3

fix 1 all nve

fix 2 all langevin 298 298 0.01 904297

fix 3 all temp/rescale 1 298 298 0.01 1 units box

displace_atoms Water move 0 0 -3 units box

dump 9 all xyz 10000 dM5.xyz

dump 10 all image 10000 pM5.*.jpg type type

run 10000