- 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.
- 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).