From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Mon Mar 28 2011 - 16:00:25 CDT
Thanks a lot JÃ©rÃ´me! I'll go for your suggestion with the carbonyl
Carbons and after moving "wrapAround" to the right codeblock it
On Mon, Mar 28, 2011 at 20:50, JÃ©rÃ´me HÃ©nin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
> On 28 March 2011 18:36, Bjoern Olausson <namdlist_at_googlemail.com> wrote:
>> For now my bins differ from 60 to 70000 Structures after 10ns.
>> I'll see what happens after 100ns. But since I doubt there is a better colvars
>> selecction I guess I have to deal with slow-relaxing, orthogonal degrees of
>> Or would you suggest another colvar selection?
>> I'll shortly summarize my setup:
>> Homodimer with 2423 Atoms the linker between the monomers is only a few ~5
>> Aminoacids long. For the sake of speed I have only choosen the C-Alphas and
>> the according Protons since I am using shake so my setups is as follows:
> You can save atoms (hence time) by using carbonyl carbons instead of
> the CA-HA pair. Actually, recent tests indicate that you could just
> remove the HAs from your current setup and things would be fine, i.e.
> the "orthogonality to constraints" requirement apparently does not
> apply to the current code (unlike early implementations, constraint
> forces seem to be accurately accounted for - however the theory for
> this has not been properly derived yet). I recommend the carbonyl
> And since you are dealing with large motion, slow diffusion could be a
> large part of the problem. Splitting things into a few windows is
> likely to help at least a bit.
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