Hello Dear Neha,
You might want to check this paper:
Sampling of slow diffusive conformational transitions with accelerated
molecular dynamics. J. Chem. Phys.,127, 155102(2007).
It tested different aMD modes (including total boost, torsion boost only
and dual boost approach) on a small peptide system and explained why the
different outcomes. Hopefully it will help you determine which aMD mode
you want to use, based on the actual situation of your own system.
Best,
Jane
On Fri, Apr 12, 2013 at 9:20 AM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> Hi Drs. Walker and Carlos,
>
> Thanks for your suggestions. As correctly pointed out, I have merged two
> issues. One is the convergence criteria and secondly I am looking at
> protein folding. I am not aware of any papers on use of aMD for disordered
> proteins however, my peptide is similar to the system reported by Hamelberg
> group (proline rich peptide- *Journal of the American Chemical Society*,
> 127, 1969-1974 and Biochemistry, 2011, 50 (44), pp 9605–9615).
>
> Prof. Walker: I am applying boost to the whole potential with an extra
> boost to the torsions (iamd=3). Do you reconn I should switch to iamd=1?
>
> Many thanks,
> Neha
>
>
>
>
>
>
> On 12 April 2013 23:10, Ross Walker <ross.rosswalker.co.uk> wrote:
>
> > Hi Neha,
> >
> > Further to what Carlos suggests I am not convinced that aMD is a good
> > choice of protocol for protein folding simulations which is essentially
> > what I believe you are doing here. Firstly if you select your boost
> poorly
> > you can end up just completely unfolding your protein. You might want to
> > check the literature and see if anyone has successfully applied aMD to
> > disordered proteins and see if there was anything special they needed to
> > do. Also are you boosting everything or just the dihedrals? The latter is
> > probably appropriate here.
> >
> > All the best
> > Ross
> >
> >
> >
> > On 4/12/13 5:59 AM, "Neha Gandhi" <n.gandhiau.gmail.com> wrote:
> >
> > >Dear Amber users and developers,
> > >
> > >I have 3 systems with different phosphorylation sites. I am interested
> in
> > >secondary structure analyses of these systems. I am using ff10 force
> field
> > >with tip3p potential. I started conventional MD with disordered
> structure
> > >and after equilibration, ran production for 50ns (NPT) followed by aMD
> > >(accelerated MD- dual boost potential as implemented in AMBER12.2 GPU
> > >version) runs upto 300ns.
> > >
> > >I also performed conventional MD for 1 microseconds (same force field
> and
> > >ensemble as above) which showed that system (1) presence of helical
> > >structure in the centre; systems (2) and (3) had beta sheets at the N-
> and
> > >C-terminals and no helical structure. These analyses from the
> trajectories
> > >agree with the experimental data.
> > >
> > >The secondary structure analyses obtained from the aMD runs show that
> all
> > >3
> > >systems have similar helical structure for last 50 ns. These doesn't
> > >correlate with experimental data.
> > >
> > >How do I interpret these aMD results? What could be the other
> parameters
> > >which could be looked that? Does aMD has preference for helical
> structures
> > >or is the force field?
> > >
> > >Your help is appreciated,
> > >
> > >
> > >--
> > >Regards,
> > >Dr. Neha S. Gandhi,
> > >Curtin Research Fellow,
> > >School of Biomedical Sciences,
> > >Curtin University,
> > >Perth GPO U1987
> > >Australia
> > >LinkedIn
> > >Research Gate
> > >_______________________________________________
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> > >AMBER.ambermd.org
> > >http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > _______________________________________________
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> >
>
>
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Curtin Research Fellow,
> School of Biomedical Sciences,
> Curtin University,
> Perth GPO U1987
> Australia
> LinkedIn
> Research Gate
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Received on Fri Apr 12 2013 - 10:30:02 PDT
