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A Question about Normal Mode Sampling #646

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MasterLucas opened this issue Jun 11, 2024 · 0 comments
Open

A Question about Normal Mode Sampling #646

MasterLucas opened this issue Jun 11, 2024 · 0 comments

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@MasterLucas
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Dear ANI developers,

I have a question about the normal mode sampling you developed in the first ANI paper. First, is the code in the GitHub repository, I couldn't find it. Second, in the paper, what do you mean in this snippet "Next, a new conformation of the molecule is generated by displacing the energy minimized coordinates by QR, the superposition of all qiR." Should I sum the displacement of all the normal modes and then add it to the relaxed structure, or should I add the displacement of each normal mode to the relaxed structure, so that, in this case, if my molecule has 3 normal modes, the output will be three new rattled geometries, whereas in the former it would have only one rattled geometry?

Yours faithfully,

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