[CP2K-user] [CP2K:21564] Understanding Output Files and Free Energy Derivatives in CP2K Alchemical Change Tutorial

[ice ZQing]

 Has anyone noticed this?

On Wed, Jun 18, 2025 at 3:53 PM ice ZQing <zqlearn123 at gmail.com> wrote:

>   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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