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

Travis polla... at gmail.com
Tue Aug 27 15:55:40 UTC 2019


You can run the calculation over each pair of atoms either by adding 
additional observations (see the prompt responses above) or just rerunning 
the input.txt file it dumps and editing the atom indices you want to get a 
rdf for. The code below specifies the atom types you want to compute a rdf 
for. When you have a list of atoms as molecules it will save each atom type 
in a list of X=1, 2, 3, 4, ..., N. It will tell you that 1='C', 2='O', etc. 
based on the order it first finds each type in your XYZ file. You pick from 
that list a reference molecule (the X in g(r) or X-Y) and then later pick 
the Y from the same list. This is equivalent to 'name X' 'name Y' in VMD.

rdf # choose rdf
n # advanced options, you can explore this later
X # where X is a number corresponding to the reference atom type
1 # intermolecular
Y # where Y is a number corresponding to the observed atom type
0 # take reference atom from atom type X
1 # take observed atom from atom type Y

On Tuesday, August 27, 2019 at 12:43:01 PM UTC-3, Ant wrote:
> 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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