fixing the protein during minimization

From: Mert Gür (gurmert_at_gmail.com)
Date: Mon Nov 09 2009 - 08:22:24 CST

Hi everyone,

In the NAMD tutorial, regarding minimization-equilibration for an NPT
ensemble, it states that
"For instance, one typically minimizes the system and then
equilibrates with the atoms in the protein fixed in space, and then
minimizes the system again and equilibrates again".

I totally understand the idea behind this statement. My problem is as
follows:

What would be the difference in keeping and not keeping the protein fixed
in space during the first minimization cycle (Still keeping the protein
fixed during equilibration).
I am asking this question because I wonder if there is any difference for
the protein to be minimized in an equilibrated water box and in an not
equilibrated waterbox. Or is the minimization of the protein independent of
the water molecules around ?

Best,

Mert

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