[CP2K-user] [CP2K:21718] Alchemical change: how to set up atom mapping for complete molecule deletion (e.g., methane solvation free energy)

[Que Zhu]

I'm sorry, I'm not getting what you're saying, do you mean to make two
structures, one containing CH4 and the other not?

ice ZQing <zqlearn123 at gmail.com> 于2025年7月31日周四 16:25写道：

> 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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