Re: Rotate two linked proteins against each other and calculate energy profile

From: Bjoern Olausson (
Date: Mon Mar 28 2011 - 16:00:25 CDT

Thanks a lot Jérôme! I'll go for your suggestion with the carbonyl
Carbons and after moving "wrapAround" to the right codeblock it

Thanks again!

On Mon, Mar 28, 2011 at 20:50, Jérôme Hénin <> wrote:
> On 28 March 2011 18:36, Bjoern Olausson <> 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
>> freedom.
>> 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
> trick.
> 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.
> Cheers,
> Jerome

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