AMBER Archive (2005)

Subject: Re: AMBER: Dummy Atom Types on both states

From: Julien Michel (j.michel_at_soton.ac.uk)
Date: Tue Feb 15 2005 - 10:10:34 CST

Hi,

If you have enough resources, you should run the same simulation different
times using different starting conformations/random seeds. You may however,
make the vexing discovery that the resulting set of free energies are
more spread than the hysteresis on a single run would have suggested ... 

-- 
Julien Michel
University of Southampton
Department of Chemistry
Dr J. W. Essex group 

> Hello,
> I have a relevant question. Since dummy atoms can only be in one state
> (lambda = 1), if we want to estimate the error of free energy calculation,
> should we use different starting conformations to redo the calculation,
> instead of doing in the "forward" and "reverse" direction?
> Thank you very much!
> Yipin
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