question about equilibration step

From: Audrey Salazar (alsalazar_at_northwestern.edu)
Date: Thu Aug 23 2007 - 17:33:03 CDT

Hello,
I am a NAMD novice and I am also new to molecular dynamics simulations. My
questions will be labeled with **.

It is my understanding that in molecular dynamics simulations an
equilibration and a production state are required. The equilibration step
ensures that the starting conformation in the production step is as its name
suggests, equilibrated, and that if the equilibration time is too short,
then the results from the production step will be junk (for example, the
properties of interest either will not stabilize or will stabilize to vastly
different values every time the same md simulation is run). I am also under
the understanding that the equilibration step and the production steps can
be done in different ensembles.

** In the .conf file, does "minimize" work for the equilibration step? What
ensemble is the minimization performed in? Can I choose it?

** Other than letting a simulation equilibrate for a long time, is there
other NAMD output that I can use to gauge whether equilibrium has been
reached?

I hope that this is clear and I look forward to any direction that you might
be able to provide.

Thank you in advance.

Audrey

-- 
Audrey L. Salazar
Amaral Research Group
Dept. of Chemical and Biological Engineering      Phone: 847.491.2188
Northwestern University
Evanston, IL USA

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