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

Ant ant... at gmail.com
Mon Aug 26 09:52:15 UTC 2019


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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20190826/14fb1b4a/attachment.htm>


More information about the CP2K-user mailing list