From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Fri Jan 15 2010 - 06:53:51 CST
They were probably referring to nonbonded exclusions (originally a
CHARMM feature). They can be specified by a NNB section at the end of
the PSF file. One convenient way to build such a section to exclude
interactions between two groups is to use alchemify
(http://www.edam.uhp-nancy.fr/Alchemify/), pretending that each of the
groups is an alchemical end-point state. The web page has more info.
2010/1/15 Charles Zhao <cicero225_at_yahoo.com>:
> I have heard from some people I have spoken to that it is possible to
> convince namd to ignore interactions between certain groups of atoms in a
> system (i.e. between peptide B and C, but not between B and A or C and A).
> This would in fact be quite useful to me. However, it seems like a vague
> idea, and they themselves do not remember clearly how it is done. I have
> not been able to find any documentation regarding anything like this. Is
> this indeed possible, or am I mistaken?
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