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How to obtain factors for the virtual site constructions? #25

Answered by ricalessandri
Clare-xiong asked this question in Q&A
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Hi @Clare-xiong and thanks for the question. The factors for the virtual sites constructions are obtained in the same way as the bond length and other bonded parameters, i.e., by comparing the mapped distributions coming from all-atom simulations to the CG distributions, as described in tutorial to parametrize new small-molecules (around section 7)). Namely, in deriving the factors for building the virtual sites, you should consider them as actual particles and hence have bond lengths between the particles and the virtual sites and match such bond lengths (even though you won't have such bond lengths in the final model). Actually, a chapter we recently published describes in quite some de…

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This discussion was converted from issue #23 on April 11, 2023 14:10.