[CP2K-user] Thoughts on RDFs for NPT ensemble simulations?

[Omar Abou El Kheir]

In the following link 
,https://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/, you can find more 
about how to update automatically the box. I'd never used it before but i 
think you can use the command -stride.


Il giorno lunedì 26 agosto 2019 11:52:16 UTC+2, Ant ha scritto:
>
> I'm quite new to molecular dynamics.  I'm struggling with how to deal with 
> RDFs for CP2K NPT simulations where the volume is distinct at each time 
> step.  If anyone could point me to online resources that discuss this or 
> provide an opinion on my approach so far, I would be very grateful.  It has 
> surprised me to find that there are very few mentions of this issue online, 
> so maybe I'm not using appropriate search terms or there is a standard way 
> of dealing with this that I'm not aware of.
>
> I have several sets of NPT simulation results and have been postprocessing 
> them in VMD.  As most of you probably know, VMD allows plotting of RDFs via 
> Extensions/Analysis/Radial Pair Distribution Function g(r).  It is a GUI 
> where only one volume value can be entered for a simulation.  
>
> My approach so far has been to enter an average volume value for a 
> simulation in the hope that the resulting RDF will be more or less accurate 
> for a long enough simulation.  I feel uncomfortable about doing this, 
> however,
>
> It would be great to know if there's a way in VMD, maybe via the terminal, 
> to import volume data and use the correct volume at each time step.  Or if 
> there's another piece of software that works on Linux or Mac that works for 
> this. Thank you.
>
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