[CP2K-user] [CP2K:18002] Re: Periodic and non-periodic box

[captain mus]

Hi Matt 

Thank you for your response, I will try it. btw I actually follow the 
instruction from your youtube channel. thank you for making a great video.

Best Regards
MuS

On Tuesday, November 1, 2022 at 9:39:36 PM UTC+7 mattwa... at gmail.com wrote:

> 1) not that I am aware of. You can specify molecules and wrap them 
> together somehow in VMD I seem to remember.
> 2) you need to make sure your molecules are connected in the non-periodic 
> direction. You can use
> &TOPOLOGY
>       CENTER_COORDINATES
> to center the atoms in the cell. If the molecules are connected together 
> then that should work once the cell is large enough.
> Matt
>
> On Sunday, 30 October 2022 at 08:11:09 UTC captai... at gmail.com wrote:
>
>>
>> Dear CP2K users and developer
>>  I'm new in CP2K and my question are: 
>> 1) Is there any way to print out the xyz file with the molecules ordered 
>> inside the box because every time I run, it always print out in an 
>> unordered way and to make it ordered I have to wrap it via VMD (see 
>> input-1). 
>>
>> 2) I want to perform a non-periodic in Z direction, My first attempt is 
>> to increase the unit cell (MULTIPLE_UNIT_CELL) by 2 or 3, but again as I 
>> mention in the first question the output is unordered and when I use wrap 
>> (VMD) it simply wrap it based on the value I seed for the pbc set. My 
>> second attempt is to make only periodic in XY via POISSON and  CELL (see 
>> input -2)  but I got an error stated that "* A non-periodic calculation 
>> has been requested but the system size exceeds the cell size in at least 
>> one of the non-periodic directions!*" any advice ?
>>
>> Thank you very much for your answer
>> Kind regars
>> MUS
>>
>

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