I’ve been having an issue with employing shear on a system of particles with a hybrid potential of DPD/tstat and LJ/cut (though I’ve encountered the same problem using just LJ/cut and NVT/SLLOD) in a cubic box with periodic boundaries in all dimensions. For visibility purposes, I’ve been shearing perpendicular to a polymer bilayer. The deform is applied to xz. As time evolves, the bilayer, which spans the dimension perpendicular to the shear direction, moves horizontally as a whole, but does not become skewed or disrupted. After 50,000 steps, the bilayer suddenly deforms, skewed in the opposite direction. It again moves horizontally, this time for 100,000 steps, then is skewed suddenly again in the opposite direction to the movement. This process continues ad infinitum.
I understand why the skewing (or tilting) is occurring in the opposite direction, as a tilt distance equal to box_dim/2 is first reached, then reset to -box_dim/2 and tilted until it reaches box_dim/2 again. What I do not understand is why I do not observe a velocity profile in the shear direction. The net effect is that my bilayer is becomes tilted, deformed, and broken up in the opposite direction to the applied shear and, more importantly, in a discontinuous manner.
Also, I’ve scatter plotted all combinations of vx, vy, vz vs x, y, z, and observe no velocity profile. Do the dump velocities have the shear profile subtracted?
Triclinic displacements are set to 0.0 in the input file for xy xz and yz.
Relevant simulation parameters:
fix integrate all nve # ( though I’ve also tried nvt/sllod)
fix shear all deform 1 xz erate 0.001 remap v
I apologize if I missed something important in the documentation causing a simple novice mistake.