Re: Excluding interactions?

From: Jérôme Hénin (
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
(, pretending that each of the
groups is an alchemical end-point state. The web page has more info.


2010/1/15 Charles Zhao <>:
> 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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