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

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Mon Mar 28 2011 - 11:36:13 CDT

On Monday 28 March 2011 18:07:43 Jérôme Hénin wrote:
> Hi Bjoern,
>
> Ajasja has given a good set of answers already, so I'll just add one
> comment.
>
> > If a bin is poorly sampled, one can interpret this as a highly unfavored
> > conformation or the applied force was not sufficient to push the
> > structure into this conformation and the process might not be
> > reversible. Is this assumption right (assuming that the sampling time
> > was sufficient)?
>
> If a region is still poorly sampled after a long time, it usually
> indicates failure to converge due to slow-relaxing, orthogonal degrees
> of freedom - that's the toughest and most common problem. It means
> that the choice of colvars is maybe not appropriate for this problem.
> Another possible cause is sow diffusion through a very broad region of
> colvar space - in this case, splitting that space into windows and
> running separate ABF simulations will help a lot.
>
> Best,
> Jerome

Thanks a lot for the explanation.
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:

  dihedral {
    group1 {
      atomnumbers { (146 Atoms for Monomer A) }
    }
    group2 {
      atomnumbers { (6 Atoms for the linker on the Monomer A site) }
    }
    group3 {
      atomnumbers { (8 Atoms for the linker on the Monomer B site) }
    }
    group4 {
      atomnumbers {(148 for Monomer B)}
    }
  }

Cheers,
Bjoer

-- 
Bjoern Olausson
Martin-Luther-Universität Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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