[CP2K-user] Molecules moving out of simulation cell in AIMD simulation

Travis polla... at gmail.com
Mon Oct 7 15:01:01 UTC 2019


CP2K dumps unwrapped coordinates, so they are not imaged back into the box 
if they drift beyond. A simple way to get a wrapped trajectory is to dump 
DCD files during MD, then use the dumpdcd.f90 script in tools/ to dump a 
wrapped DCD (-pbc option). I don't recommend writing XYZ format 
trajectories for MD. Write DCD and convert. Way easier to strip info than 
to add it back in.


On Monday, October 7, 2019 at 8:09:09 AM UTC-3, Harender Singh wrote:
> Dear all, 
> I am running AIMD simulation of some electrolyte at Li electrode. While 
> the electrolyte molecules are staying within the simulation cell, the 
> electrode atoms are moving out of the cell. 
> Is there any possible explanation for that?
> Is there something wrong with my simulation setup? If yes, then how can I 
> correct it?
> Thanks for the help in advance. 
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