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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Nov 18 2012 - 14:00:02 PST
