[CP2K-user] [CP2K:21694] 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

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