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

[farzaneh sarrami]

Thanks Travis,

Would you please explain in more details how can I use dumpdcd.f90 script 
in cp2k ? as I have same problem.

Best,
Farzaneh

On Monday, October 7, 2019 at 5:01:01 PM UTC+2, Travis wrote:
>
> Hi,
>
> 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.
>
> -T
>
>
> 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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