[gmx-users] Assignment of new velocities for multi-runs
jalemkul at vt.edu
Sat Sep 29 18:57:48 CEST 2012
On 9/29/12 8:47 AM, James Starlight wrote:
> Peter, Justin,
> Thanks alot for the comments.
> In the current work I do short simulation of the membrane receptors (
> 100 ns) started from different conformations of that proteins in the
> common physical conditions and than do Essential Dynamics analysis of
> the calculated trajectories and compare eigenvectors from both of
> them. It's intresting to me might the different starting velosities
> influence on the overal dynamics of the protein- i.e sampling of
> different sub-states ( which would reflect on the eigenvectors from
> that runs)
If different simulations do very different things, you can't conclude much. If
there is overlap in the ensembles of independent simulations, then you can make
better conclusions. The purpose of different starting velocities is to improve
sampling, such that you can observe converged results across multiple
simulations that come from "independent" starting points.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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