[CP2K-user] [CP2K:21552] Understanding Output Files and Free Energy Derivatives in CP2K Alchemical Change Tutorial

[ice ZQing]

  Hi everyone,
I'm currently learning to perform molecular simulations with CP2K, and I’ve 
been following the official Alchemical Change (AC) tutorial, located at:  
  cp2k/tests/FE/regtest-1/  or cp2k/tests/FE/regtest-1 at master · cp2k/cp2k 
<https://github.com/cp2k/cp2k/tree/master/tests/FE/regtest-1>  
Using *CP2K version 2022.2*
  The tutorial simulates an alchemical transformation between two molecular 
fragments in water, where the main difference is the presence or absence of 
a *hydrogen atom*, likely in an alanine residue (ACE–ALA–NME) solvated by 
water. I try this simulation using the GENMIX method and runs a trajectory 
of *20,000 steps at λ = 0.5* with classical force fields (FIST).  
  I have a few questions regarding the output and how to process the 
results:
What does these Output files mean and which are important for free energy 
analysis? After the run, I get the following files:
Solv_alch_chng-1.ener
Solv_alch_chng-1.restart
Solv_alch_chng-mix-1.ener
Solv_alch_chng-pos-1.pdb
Solv_alch_chng-r-1.out
Solv_alch_chng-r-2.out
    I assume:
*.ener contains energy data,
*.pdb is trajectory,
*.restart is for restarting.
But I’m not sure what the* -r-1.out, -r-2.out, and -mix-1.ener files* are 
for, or what physical quantities they contain. Also, the .ener files 
contain only a few columns of data, with no clear labels, so I’m not sure 
how to interpret them.
Which of these output files are necessary for post-processing the free 
energy difference? And what is the best way to extract or average relevant 
observables like free energy gradients?
 I’m happy to share my input files if needed.  

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