Rerun command and post processing


  1. I didn’t calculate anything while running the simulation just to calculate everything after the simulation. I tried to use the rerun command to read the dump file.
    I am not sure if we need to use everything like before(when we rand the simulation) except we replace run with rerun?

I constantly get the fix ave/time missed step. I have my trajectory saved every 500 step(500*1fs). I tried to print the output every 1000 step but it gave me that error.

  1. My second question is the post processing. I kind of unsure about the wrapped coordinated and the unwrapped coordinates. If we calculate any thermodynamic quantity or dynamical variable on the fly (diffusion
    coefficient) and calculate the same afterward after wrapping the coordinates (post processing), will it be different? Also, it would be highly appreciated if anyone has done post analysis of the h-bond(without using drieding potential)
    and know how to do it. As a new learner, I don’t have much knowledge of coding at the moment (thought it is a must thing in computer simulation).

Thank you,

A better debug would be to calc everything you want during
the run and save dump files. Then see if you can write a
script that computes the same values

using rerun to read the dump files.

W/out seeing your fix ave/time command, no one
can say why it is giving an error. Probably b/c it
needs values on many steps to produce output
on step 1000.

The rerun and read dump commands can account
for wrapped vs unwrapped coords, so in principal

something you calc should not be different.

For h-bonds, you will probably have to do the
rerun script with the dreiding potential. I can’t
think of any other feature in LAMMPS that calcs
h-bonds. Unless you just want a simple distance-based

tally of H pairs or the like.