[gmx-users] Hamiltonian Replica Exchange

Thomas Evangelidis tevang3 at gmail.com
Tue Jun 24 22:32:26 CEST 2014


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.




Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens

email: tevang at pharm.uoa.gr

          tevang3 at gmail.com

website: https://sites.google.com/site/thomasevangelidishomepage/

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