[CP2K-user] [CP2K:12401] How to plot RDFs for NPT simulations?

[Josip Lovrić]

Put output to .crd file for example.

On Wed, Oct 23, 2019, 11:22 AM Ant Stone <ant... at gmail.com> wrote:

> Thank you, Josip.  Yes, I just checked it out.  Unfortunately, I don't see
> how it's possible to combine CP2K's .xyz and .cell files there to generate
> an RDF.
>
> There's a function at MDAnalysis called something like "InterRDF" and its
> arguments appear to be atom types.  Maybe I'm missing something, but I
> don't see how to either correct our CP2K .xyz trajectory files according to
> our .cell files using MDAnalysis.
>
> On Wed, 23 Oct 2019 at 10:09, Josip Lovrić <josip7... at gmail.com> wrote:
>
>> Have you checked mdanalysis? They have nice libraries for reading data
>> and also analyze.
>>
>> Josip
>>
>> sri, 23. lis 2019. u 11:05 Ant <ant... at gmail.com> napisao je:
>>
>>> I am re-posting a question I already asked in the hope that someone who
>>> can help will see it.
>>>
>>> I already have NPT simulation results and would like to plot RDFs.  I
>>> usually use VMD, but the RDF GUI only allows a single set of cell
>>> parameters.  I need to be able to enter a distinct set of cell parameters
>>> at each time step.
>>>
>>> Does anyone know whether it is possible to do this in VMD or if there is
>>> another piece of software that can do it?  I have not found anything in my
>>> own searches.  Thank you.
>>>
>>> --
>>> 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 cp... at googlegroups.com.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/cp2k/a3b9d101-d815-4a85-b54e-c7879bda352d%40googlegroups.com
>>> <https://groups.google.com/d/msgid/cp2k/a3b9d101-d815-4a85-b54e-c7879bda352d%40googlegroups.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>> --
>> 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 cp... at googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/cp2k/CAHy4cn8Z%2BS3ek2kC1S3TaGRApQTsqXWs-1Ebbi0uiMKxfC55TA%40mail.gmail.com
>> <https://groups.google.com/d/msgid/cp2k/CAHy4cn8Z%2BS3ek2kC1S3TaGRApQTsqXWs-1Ebbi0uiMKxfC55TA%40mail.gmail.com?utm_medium=email&utm_source=footer>
>> .
>>
> --
> 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 cp... at googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/cp2k/CAPc0%3DEsvkEP3VQ6r0cRjPtDT3hO%3DG4HPna2KE7Mos7XnYRy2GA%40mail.gmail.com
> <https://groups.google.com/d/msgid/cp2k/CAPc0%3DEsvkEP3VQ6r0cRjPtDT3hO%3DG4HPna2KE7Mos7XnYRy2GA%40mail.gmail.com?utm_medium=email&utm_source=footer>
> .
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20191023/d1fb6263/attachment.htm>