AMBER Archive (2008)

Subject: AMBER: Trajectory - Average Structure - Equilibration

From: dpandit_at_brandeis.edu
Date: Wed Jun 11 2008 - 14:37:46 CDT

Hi All:
After going through archives and tutorials, I am kind of confused
about what portion of the initial trajectory needs to be discarded and
what is the appropriate way to calculate average structure.
Particularly, say first I performed heating at constant volume for 20
PS. Temperature is OK. I performed constant Pressure for next 200 PS
but average pressure of the system is not yet stable. So I perform
additional 400 PS for constant pressure. Now, pressure seems OK and I
go ahead for the production runs. So do I discard first 620 PS of
trajectory or I just need to discard 20 PS.

Archive Message - and other messages on the link

http://structbio.vanderbilt.edu/archives/amber-archive/2008/1257.php

Tutorials
http://amber.scripps.edu/tutorials/basic/tutorial3/section6.htm

http://amber.scripps.edu/tutorials/advanced/tutorial8/loop13.htm

Thank you.
Deepa

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