AMBER Archive (2000)

Subject: calculation time

From: Andrew Aird (a.aird_at_physik.uni-stuttgart.de)
Date: Mon Oct 23 2000 - 05:49:27 CDT

        Hello
I'm new in the field of MD and have only recently started working with Amber 5.
I'm trying to simulate a system consisting of three proteins (GFPs), each
connected by a linker (10 amino acids) to a "central" protein-trimer (TRAF2)
I'd like to do a simulation with explicit solvent. But since I'm working on a
single processor PC, this would take a lot of time... I'm trying to minimize
the calculation time!

MY QUESTION:
At the moment, I'm only interested in the relative positions (distance and
orientation) of the three GFPs compared to the TRAF2.
Is it possible to "freeze" the internal coordinates of the GFPs and the
TRAF2-trimer, so that each of the proteins can only move as a whole?

Thank you for your help in advance

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Andrew Aird
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