[CP2K-user] [CP2K:21719] Alchemical change: how to set up atom mapping for complete molecule deletion (e.g., methane solvation free energy)

[ice ZQing]

Yeah, that's exactly what I mean.

Que Zhu <wanghong.id at gmail.com> 于 2025年7月31日周四 16:38写道：

> 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
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "cp2k" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to cp2k+unsubscribe at googlegroups.com.
>>> To view this discussion visit
>>> https://groups.google.com/d/msgid/cp2k/aef30ccc-039b-41ae-8719-906d38ac4ec5n%40googlegroups.com
>>> <https://groups.google.com/d/msgid/cp2k/aef30ccc-039b-41ae-8719-906d38ac4ec5n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "cp2k" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to cp2k+unsubscribe at googlegroups.com.
>> To view this discussion visit
>> https://groups.google.com/d/msgid/cp2k/CA%2BwCwGkPgYz5FTeMUhxKbwY6gEApaJtgYEhsvZUk5VmAq0vRYQ%40mail.gmail.com
>> <https://groups.google.com/d/msgid/cp2k/CA%2BwCwGkPgYz5FTeMUhxKbwY6gEApaJtgYEhsvZUk5VmAq0vRYQ%40mail.gmail.com?utm_medium=email&utm_source=footer>
>> .
>>
> --
> You received this message because you are subscribed to the Google Groups
> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to cp2k+unsubscribe at googlegroups.com.
> To view this discussion visit
> https://groups.google.com/d/msgid/cp2k/CAD%2B_nUtaxCjwLBHe8euKpEo%3DqJQMC1hv8a_ZRPTyavaquQL_HQ%40mail.gmail.com
> <https://groups.google.com/d/msgid/cp2k/CAD%2B_nUtaxCjwLBHe8euKpEo%3DqJQMC1hv8a_ZRPTyavaquQL_HQ%40mail.gmail.com?utm_medium=email&utm_source=footer>
> .
>

-- 
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/cp2k/CA%2BwCwGm6nc7E6CLPuOX2Z8hg9-BzpVfTGcBX3Nz%3DmF5sPTzhkg%40mail.gmail.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20250802/51520e1e/attachment.htm>