Hi Romelia,
It happens both, but the dissociation of the dimer is more noticeable. The
dimer is a helical bundle and as the helices start to bend it dissociates.
thanks,
Thomas
On 19 November 2012 18:35, Romelia Salomon <romelia.caltech.edu> wrote:
> Dear Thomas
>
> One quick question first, is it unfolding the secondary structures or
> separating the two components of the dimer?
>
> Best wishes,
>
> Romelia
>
> > Dear Romelia and other AMBER users/developers,
> >
> > Thanks for the clarification. I have tried the rule of thump to select E
> > and alpha values, which is described both in the recent paper you cited
> > and
> > the manual. Namely, to decide the dihedral boost parameters (Ed, aD) and
> > the potential boost parameters (Ep, aP) I did:
> >
> > Ed=Ed_average+4*ResNum
> > aD=4*ResNum*0.2
> > Ep=Ep_average+0.16*AtomNum
> > aP=0.16*AtomNum
> >
> > However, these parameter values lead to the unfolding of my protein
> dimer.
> > I have also tried setting aD=4*ResNum*0.4 but I still observe the same
> > effect.
> > How would you recommend making the boost smoother? By increasing just the
> > alpha values? Do I need to increase both of them?
> >
> > thanks in advance,
> > Thomas
> >
> >
> >
> >
> > On 27 September 2012 01:27, Romelia Salomon <romelia.caltech.edu> wrote:
> >
> >> Hi Thomas
> >>
> >> I added comments to your questions bellow.
> >>
> >> > Dear Amber users,
> >> >
> >> > I want to monitor the dynamics between a hetero-dimeric helical bundle
> >> and
> >> > a peptide. It is believed that the peptide binds at the
> >> protein-protein
> >> interface of the dimer and unwinds the helix of one of the components.
> >> For
> >> > this purpose I am considering accelerated MD (aMD) but have some
> >> queries
> >> about it:
> >> >
> >> > 1. Unlike Metadynamics, the bias in the potential is not history
> >> dependent,
> >> > therefore the system may explore multiple times the same area of
> >> conformational space. Is this correct?
> >>
> >> This is correct, AMD will make it more probable to move out of deep
> >> stable
> >> basins in the conformational space and there is no mechanism to prevent
> >> it
> >> from going back.
> >>
> >> >
> >> > 2. Is it possible to find the predominant conformations of the complex
> >> from
> >> > an aMD trajectory, namely the ones that we would expect to observe the
> >> most
> >> > in an unbiased MD trajectory?
> >>
> >> Yes, what you will get in the end of the AMD calculation is a state
> >> distribution, that although is not the unbiased (canonical) one, it
> >> still
> >> holds some resemblance to it. AMD distributions can be re-weighted to
> >> produce Boltzmann distributions.
> >>
> >> Please refer to these papers for more information.
> >> (a recent paper we just published on the GPU implementation of AMD)
> >> http://pubs.acs.org/doi/abs/10.1021/ct300284c
> >> (one of the main papers for this method)
> >> http://www.cse.nd.edu/~izaguirr/HaMM04.pdf
> >>
> >>
> >> I hope this helps, let me know if you need more information.
> >>
> >> Best,
> >>
> >> Romelia
> >
>
>
> --
> ****************************************
> Romelia Salomon
> Walker Group
> 398 San Diego Supercomputing Center
> UC San Diego
>
>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Mon Nov 19 2012 - 09:00:04 PST
