Dual topology questions

From: Randall Hall (randall.hall_at_dominican.edu)
Date: Mon Mar 01 2021 - 20:01:52 CST

  I want to make sure I understand a detail of the NAMD implementation of the dual topology FEP algorithm. With alchDecouple off, is the following correct?

1) all bonds, dihedrals, angles, and impropers are not scaled for any value of lambda

2) non-bonded interactions between atoms in annihilated are scaled with lambda

Thanks in advance for helping me understand these details.


Randall Hall (he/him)
Lillian L.Y. Wang Yin, Ph.D. Endowed Professor of Chemistry
Dominican University of California
220 Science Center
Phone: 415-482-1911
Fax: 415-482-1972

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