[CP2K-user] Can I calculate the internal energy from NPT simulations or does the thermostat complicate things?

[Ant]

I would be very grateful if someone could help me out with what is probably 
a newbie question.  I have been unable to find the answer in text books or 
online, however.  

I have existing NPT simulation results that I used to calculate density. 
 My question is, can I also use them to calculate the internal energy?  

I know that for an NPT simulation, the "conserved quantity" (column 6 of 
the .ener file) is *not* internal/total energy.  It is the energy of the 
system + the energy of the thermostat + the energy of the barostat. 
 However, is it a reasonable approach to calculate the internal energy by 
summing the potential and kinetic energies (columns 3 and 5, .ener file)? 
 Or does the added energy from the thermostat somehow mess things up?  

I found a paper where someone first ran CP2K NPT simulations and then used 
the cell volumes to run NVT simulations to get the internal energy (I 
assume because the fluctuations in V would be quite large for NPT and might 
lead to error in internal energy--my internal energy averages from my NPT 
simulations seem quite stable though).  So someone has used a non-NVE 
approach.  However, I have a niggling feeling that the thermostat might be 
doing something I don't understand.  Thank you.

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