[gmx-users] Different initial conditions for the membrane protein simulation

James Starlight jmsstarlight at gmail.com
Mon Sep 10 18:36:39 CEST 2012

Dear Gromacs Users!

I'm simulating intrinsic dynamics of some membrane receptors which can
have functional relevance. Therefore I'm looking for the most suitable
initial conditions of my simulation which could provide maximal degree
of such dynamics (arisen from the cooperative thermal fluctuations for
instance). As I know the proper chosen thermostat can significantly
influence on the overall dynamics of the protein. In particular I've
found that Noose-Hover thermostat can promote it significantly. But
there are some theoretical studies which suggest that Nose-Hover
thermostat can produce alot of artifacts due to the incorrect energy
distribution on the micro-states. So the dynamics produced onto such
trajectories can be unphysical in general. That authors also suggest
use collision thermostat ( in GROMACS usage of SD integrator
correspond to that conditions without any t_coupl ).
So the main question- IS there any way to observe impact of each
thermostats and other initial conditions on the overall dynamic
behavior of the protein. For example does it possible to make some
energy landscape of the trajectories calculated from different
conditions to compare thermal energy distribution on the micro-states?
Finally is there any way to compare such energy landscapes with the
conformational maps ( e.g projections onto some lowest Principal
components) to direct monitor the energy contribution of each
conformation ?

Thanks for help,


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