Re: Excluding interactions?

From: Jérôme Hénin (
Date: Sat Jan 16 2010 - 12:37:26 CST

That is correct, if you want to involve more than two groups,
Alchemify won't do it for you. If you can do a bit of programming
though, I recommend to try and adapt the Alchemify code to do exactly
what you want. It is probably the easiest way.

2010/1/16 Charles Zhao <>:
> 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 <>
> To: Charles Zhao <>
> Cc:
> Sent: Fri, January 15, 2010 4:53:51 AM
> Subject: Re: namd-l: Excluding interactions?
> Hi,
> 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.
> Jerome
> 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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