[gmx-users] Hamiltonian Replica Exchange

[HANNIBAL LECTER]

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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