[CP2K-user] [CP2K:16423] How to make sure my molecules stay in the initially given cell in a CP2K simulation?

[Thomas Kühne]

Dear Bence Baranyi, 

I do this either directly inside my own post-processing analysis tools, or via the PBCTools 
plug-in within VMD: https://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

Best, Thomas Kühne

> Am 03.01.2022 um 18:17 schrieb Bence Baranyi <babuteck at gmail.com>:
> 
> Dear Thomas Kühne,
> 
> thank you for your answer! Is there a way to fold the molecules back after the simulations? I need them to be in the original box since the box was chosen for a specific density of ammonia. I know, for example, GROMACS has an easy way to do this, but I don't know how to make this happen in CP2K.
> 
> Best regards,
> Bence Baranyi
> On Thursday, December 16, 2021 at 11:08:17 AM UTC+1 tkuehne wrote:
> Dear Bence Baranyi, 
> 
> the coordinates in the output file are not folded back into the simulation box. 
> CP2K intern, however, periodic boundary conditions are strictly enforced, so 
> your „molecules stay in the initially given cell“. 
> 
> Best, 
> Thomas Kühne
> 
> 
>> Am 16.12.2021 um 11:01 schrieb Bence Baranyi <babu... at gmail.com <applewebdata://DB1404D5-CDCB-4ABB-B066-C3C26EC9103C>>:
>> 
> 
>> Hi!
>> I would like to make a simulation in CP2K, using AM1 on a system containing 33 NH3 molecules, in a cell with 10.855 angstroms as side length and with periodic boundary condition. My aim with this simulation is to get from randomly generated molecule positions to a somewhat realistic arrangement to be used later in an AIMD simulation. How can I ensure that the molecules stay in the said cell during the simulation? I attached the last structure of the simulation (and my input file) and as you can see the max distance between two molecules is clearly bigger than what it could be in a box with 10.855 angstrom sides.
>> All help is appreciated!
>> 
> 
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>> <cp2k_am1_33nh3_last.txt><bulk_33nh3.inp>
> 
> ==============================
> Thomas D. Kühne
> Dynamics of Condensed Matter
> Chair of Theoretical Chemistry
> University of Paderborn
> Warburger Str. 100
> D-33098 Paderborn
> Germany
> thomas... at upb.de <applewebdata://DB1404D5-CDCB-4ABB-B066-C3C26EC9103C>
> +49/(0)5251/60-5726 <tel:+49%205251%20605726>
> 
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==============================
Thomas D. Kühne
Dynamics of Condensed Matter
Chair of Theoretical Chemistry
University of Paderborn
Warburger Str. 100
D-33098 Paderborn
Germany
thomas.kuehne at upb.de
+49/(0)5251/60-5726

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