Alchemical change: how to set up atom mapping for complete molecule deletion (e.g., methane solvation free energy)

[ice ZQing]

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

[ice ZQing]

Could someone please address my questions?

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[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 <zqlea...@gmail.com> 于2025年7月31日周四 16:25写道：

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[ice ZQing]

Yeah, that's exactly what I mean.

Que Zhu <wangh...@gmail.com> 于 2025年7月31日周四 16:38写道：

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[ice ZQing]

Apologies for the follow-up.  I would like to confirm whether you have noticed my previous response and would appreciate your feedback on the feasibility of the aforementioned proposal.

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