Dear All,
Recently, I have tried to use topotools and I used Axel’s manual:
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-2
I tried Step 2a: Methane, input files in.step2a and in.step2a-2
and I have found that periodic boundary conditions (PBC) are not working in this example:
molecules are outside the simulation box by the end of the simulation.
PBC were defined in the input files:
boundary p p p
Could you please help me how to properly define periodic boundary conditions?
Thank you.
Kind Regards,
Evgeniya
Dear All,
Recently, I have tried to use topotools and I used Axel's manual:
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-2
I tried Step 2a: Methane, input files in.step2a and in.step2a-2
and I have found that periodic boundary conditions (PBC) are not working in
this example:
molecules are outside the simulation box by the end of the simulation.
PBC were defined in the input files:
boundary p p p
Could you please help me how to properly define periodic boundary
conditions?
you don't need help with that. nothing needs to be changed here.
periodic boundaries are properly used. the issue is most likely due to
visualization. when you simulate with periodic boundaries, you can
either follow the original atoms as they progress, or switch to their
respective periodic copy when it leaves the original cell. that is,
you can have either an "unwrapped" or a "wrapped" trajectory. with
molecules, it is usually preferable to record an unwrapped trajectory
and then do a wrapping later on based on entire molecules instead of
apples.
axel.