[gmx-users] Assignment of new velocities for multi-runs

Justin Lemkul 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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