From: Charles Zhao (cicero225_at_yahoo.com)
Date: Wed Jan 20 2010 - 13:44:47 CST
Now that I have done this, I am unable to start a simulation without it crashing due to a "bad global exclusion count". Reading the line here: http://www.ks.uiuc.edu/Research/namd/2.6/ug/node24.html , it says "In rare special circumstances atoms that are involved in bonded terms
(bonds, angles, dihedrals, or impropers) or nonbonded exclusions (especially
implicit exclusions due to bonds) will be placed on non-neighboring
patches because they are more than the cutoff distance apart. This can
result in the simulation dying with a message of
``bad global exclusion count'', my interpretation is that this will always happen if I attempt something like this. Is it at all possible to avoid?
From: Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>
To: Charles Zhao <cicero225_at_yahoo.com>
Sent: Sat, January 16, 2010 10:37:26 AM
Subject: Re: namd-l: Excluding interactions?
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 <cicero225_at_yahoo.com>:
> 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>
> Cc: namd-l_at_ks.uiuc.edu
> 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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