Currently, I experiment with a molecular water system. I perform nonequilibrium molecular dynamics runs in LAMMPS, using the SLLOD equations of motion in conjunction with the Lees-Edwards periodic boundary conditions.

I perform NEMD simulationS for several shear rate values under the NVT ensemble to reach a steady-state. After

the system reaches a nonequilibrium steady state, I want to compute the diffusion coefficient by two different

techniques: either the Green-Kubo relations (which relate integrals of the momentum autocorrelation functions over the nonequilibrium steady-state to the diffusion coefficients directly); or the Einstein relations (which relate the unconvected mean

square displacements of the molecules at time t to products of the diffusion coefficients and t); To do so, the unconvected coordinates and the SLLOD peculiar momenta must be used.

I have understood that using the command

dump traj_dump all custom 1 file.lammpstrj id mol element type xu yu zu x y z vx vy vz fx fy fz

the convected coordinates, and the actual momenta are printed out, i.e., the terms corresponding to the external force are included.

I wonder if there is any way of directly extracting the unconvected coordinates and the peculiar velocities of the atoms every N timesteps. Are there any specific commands that I can use?

Below is the input script that I use, setting the nonequilibrium run simulation.

I really appreciate any help you can provide.

units real

atom_style full

log

dimension 3

boundary p p p

read_data restart_file

pair_style lj/cut/coul/long 10 10

kspace_style ewald 1.0e-4

pair_modify tail yes

pair_coeff 1 1 0.155297 3.16562

pair_coeff 2 2 0.0 0.000

pair_modify mix arithmetic

bond_style harmonic

bond_coeff 1 412.00935 1.0

angle_style harmonic

angle_coeff 1 45.739 109.47

special_bonds lj 0.0 0.0 0.0 coul 0.0 0.0 0.0

reset_timestep 0

neighbor 3.0 bin

neigh_modify every 1 delay 0 check yes

variable shear_rate index ${shear_rate}

fix integrator all nvt/sllod temp 300.0 300.0 100.0 # check thermostat

fix 2 all deform 1 xy vel ${shear_rate} remap v units box

dump traj_dump all custom 100 traj_${simname}.lammpstrj id mol element type xu yu zu x y z vx vy vz fx fy fz

dump_modify traj_dump sort id

run_style verlet

timestep 1

run 100000