[gmx-users] Hamiltonian Replica Exchange

[Mark Abraham]

Indeed. REST implemented in PLUMED seems a good bet.

Mark
On Jun 24, 2014 11:50 PM, "HANNIBAL LECTER" <hanniballecter13 at gmail.com>
wrote:

> I would think of using Replica Exchange with Solute Tempering in this case.
> Look at the paper as to how one can implement this in Gromacs (doi:
> 10.1002/jcc.21703).
>
> Without having more details I would suggest to you to scale the Hamiltonian
> of each replica such that the Helix bundles are always correspond to the
> low temperature hamiltonian. The solute in your case would be the
> disordered ends that moves up the replica ladders during the exchange.
>
> The lambda dynamics module should be used and I would keep the topologies
> corresponding to the two ends such that at state B the hamiltonians of only
> the disordered ends are scaled (i.e. no scaling for the helical segments).
>
>
>
> On Tue, Jun 24, 2014 at 4:32 PM, Thomas Evangelidis <tevang3 at gmail.com>
> wrote:
>
> > Greetings,
> >
> > I want to use the HREX implementation of GROMACS to study the dynamics
> of a
> > heterodimeric protein. The structure is a two helix bundle (two helical
> > monomers that are wrapped around each other) with disordered ends. I am
> > mainly interested in the dynamics of the disordered ends because I know
> > from NMR that the rest remains structured. My question is, can I scale
> > selectively the Hamiltonian of the disordered ends whilst leaving the
> > Hamiltonian of the rest of the protein untouched in order to preserve the
> > dimeric structure?
> >
> > Otherwise I 'll have to impose distance and secondary structure
> restraints
> > which will slow down the computations and render the dynamics of the
> > structured part unphysical. Is it possible to increase the force constant
> > of the harmonic restraints as lambda decreases to attenuate the stiffness
> > of the helices?
> >
> > The other alternative will be to use much fewer replicas (up to lambda
> ~0.8
> > to be on the safe side) thus with slower sampling.
> >
> > thanks,
> > Thomas
> >
> > --
> >
> > ======================================================================
> >
> > Thomas Evangelidis
> >
> > PhD student
> > University of Athens
> > Faculty of Pharmacy
> > Department of Pharmaceutical Chemistry
> > Panepistimioupoli-Zografou
> > 157 71 Athens
> > GREECE
> >
> > email: tevang at pharm.uoa.gr
> >
> >           tevang3 at gmail.com
> >
> >
> > website: https://sites.google.com/site/thomasevangelidishomepage/
> > --
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