[CP2K-user] [CP2K:16421] How to make sure my molecules stay in the initially given cell in a CP2K simulation?

[Bence Baranyi]

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>:
>
> 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!
>
> -- 
> You received this message because you are subscribed to the Google Groups 
> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to cp2k+uns... at googlegroups.com.
> To view this discussion on the web visit 
> https://groups.google.com/d/msgid/cp2k/130dff75-85a6-444c-afb2-c28618598be8n%40googlegroups.com 
> <https://groups.google.com/d/msgid/cp2k/130dff75-85a6-444c-afb2-c28618598be8n%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
> <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
> +49/(0)5251/60-5726 <+49%205251%20605726>
>
>

-- 
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/31644e8f-0b14-4b4b-9759-d7c69f058749n%40googlegroups.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20220103/6c542b35/attachment.htm>