AMBER Archive (2004)

Subject: Re: AMBER: Free energy in Amber8

From: David A. Case (
Date: Wed Jun 02 2004 - 09:35:24 CDT

On Wed, Jun 02, 2004, Jiten wrote:
> I quite do not understand the meaning of production run for the free energy
> MD. Is it has the same meaning as in Sander MD prior to the equlibration. My
> starting coordinate file is from the previously performed 1ns equlibration.
> For such case do I need to run the production for each step of the lamda
> value or just at the beginning of the peturbation when lamda=0

The jargon is this:

"equilibration" is something you do first (at each value of lambda), but
   do not use for analysis.

"production" is the part of the trajectory after the equilibration phase,
   which is used to generate estimates of free energies, etc. The production
   phase uses the restart file from the equilibration phase as a starting


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