From: Charles Zhao (cicero225_at_yahoo.com)
Date: Fri Jan 15 2010 - 21:12:23 CST
Thank you for your response. I think I understand. With this I can, for instance, remove nonbonded interactions between A and B in a psf file. However, if I then remove the interactions between C and A using the same procedure, will Alchemify keep both nonbonded exclusion lists, or erase the first one between A and B? I would of course like to have both at once. The web page is not clear on this, and it seems Alchemify can only remove the interactions between two groups at once (since that's what it was designed for).
From: Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>
To: Charles Zhao <cicero225_at_yahoo.com>
Sent: Fri, January 15, 2010 4:53:51 AM
Subject: Re: namd-l: Excluding interactions?
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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