[CP2K-user] [CP2K:21717] Alchemical change: how to set up atom mapping for complete molecule deletion (e.g., methane solvation free energy)

[ice ZQing]

Could someone please address my questions?

On Mon, Jul 28, 2025 at 8:25 PM ice ZQing <zqlearn123 at gmail.com> wrote:

> Dear all,
>
> I am currently trying to compute the solvation free energy of a methane
> molecule in water using the *ALCHEMICAL_CHANGE *in CP2K. My goal is to
> gradually "disappear" the methane molecule (i.e., turn off its
> interactions) in the aqueous environment and obtain the free energy change
> associated with this process.
>
> From the *cp2k/tests/FE/regtest-1 /Solv_alch_chng.inp*, I understand that
> ALCHEMICAL_CHANGE allows mixing different FORCE_EVALs with a
> lambda-dependent weight, and that a MAPPING section can be used to relate
> fragments between these force evaluations. However, I am confused about how
> to correctly define the mapping in the case of full molecule deletion.
>
> Specifically:
>
>    -
>
>    In my case, one *FORCE_EVAL* includes the methane molecule , and the
>    other does not contain the methane at all.
>    -
>
>    Since there is no one-to-one correspondence of atoms in the
>    disappearing methane molecule (they literally vanish), I am unsure how to
>    define the *MAPPING* section for this transformation.
>    -
>
>    The documentation suggests that fragments are used for mapping, but
>    provides limited examples and no guidance on what to do when a whole
>    fragment (i.e., methane) is absent in one of the force fields.
>
> Is it possible to perform such a transformation (from a molecule being
> present to absent) with CP2K’s alchemical change framework? If so, how
> should the mapping be handled in such a case?
>
> Any insights, examples, or suggestions would be greatly appreciated.
>
> Best regards
>
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