# Atom moving velocity regarding "displace_atoms" command

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:

units real

atom_style full

dimension 3

boundary p p p

# Atom definition

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

please note that this is a forum to discuss issues with using LAMMPS, NOT a forum to learn how to do MD simulations and to get training in doing them or have other people correct or improve your input. what is a good approach to model and extract the information you want to get from your simulations is something that depends on your specific research interest and needs and thus you should discuss with your adviser/supervisor and senior colleagues or whoever is tutoring you and also learn from studying publications of the same or similar subjects of research.

what I can tell you is, that you are using two thermostat algorithms in your simulation and that is a very bad idea. in fact, it is my opinion that fix temp/rescale should not be used in any production simulation because of its unphysical effect on systems.

axel.