<div dir="auto">Yeah, that's exactly what I mean.</div><br><div class="gmail_quote gmail_quote_container"><div dir="ltr" class="gmail_attr">Que Zhu <<a href="mailto:wanghong.id@gmail.com">wanghong.id@gmail.com</a>> 于 2025年7月31日周四 16:38写道：<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><p>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?</p></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">ice ZQing <<a href="mailto:zqlearn123@gmail.com" target="_blank" rel="noreferrer">zqlearn123@gmail.com</a>> 于2025年7月31日周四 16:25写道：<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><span style="color:rgb(42,47,69);font-family:"PingFang SC";font-size:16px">Could someone please address my questions?</span></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Jul 28, 2025 at 8:25 PM ice ZQing <<a href="mailto:zqlearn123@gmail.com" target="_blank" rel="noreferrer">zqlearn123@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><p>Dear all,</p>
<p>I am currently trying to compute the solvation free energy of a methane molecule in water using the <b>ALCHEMICAL_CHANGE </b>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.</p>
<p>From the <b>cp2k/tests/FE/regtest-1 /Solv_alch_chng.inp</b>, 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.</p><p>Specifically:</p>
<ul>
<li>
<p>In my case, one <b>FORCE_EVAL</b> includes the methane molecule , and the other does not contain the methane at all.</p>
</li>
<li>
<p>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 <b>MAPPING</b> section for this transformation.</p>
</li>
<li>
<p>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.</p>
</li>
</ul>
<p>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?</p>
<p>Any insights, examples, or suggestions would be greatly appreciated.</p>
<p>Best regards</p>
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