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

Ant ant... at gmail.com
Tue Aug 27 15:43:01 UTC 2019


Thank you very much, Travis, for all your time.  I'm sorry to impose.  

Unfortunately, if I understand you correctly, this won't work for me 
because I have multiple atom types in my system.  I have been experimenting 
with travis today and it seems like if I turn off molecule recognition, 
there's no way to differentiate between atom types 9I may be wrong).

The great thing about VMD for me is that I can calculate RDFs for (for 
example) "name H" "name H" and "name O" "name H" and "name O name O" and 
"name Si" "name O" (and so on) for every possible pair in my system, where 
the first atom in a pair is the one of interest (from which an RDF is 
calculated).  In travis, I have figured out how to switch off the 
molecules, but don't know how to define that I want RDFs for a particular 
pair pair.  I can't figure out exactly what is going on, but have a vague 
feeling that travis is calculating RDFs based on all of the atoms in the 
system, not the specific pairs I want.

It seems so odd that there isn't more available on how to deal with NPT 
RDFs in general.  I don't know if this is maybe something everyone just 
knows how to do.  Unfortunately, I don't have coworkers to ask and I hate 
troubling you.
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