AMBER Archive (2004)

Subject: AMBER: saving trajectory parameters

From: Ed Pate (
Date: Sat Nov 27 2004 - 18:17:40 CST


I want to use Amber7 to simulate the motion of an EPR spin probe bound to
a large protein, myosin. The simulation will be done as a belly
calculation. To calculate an order parameter for the simulated motion of
the probe to compare with experiment, I need the orientation of the spin
probe at every 2 fs time step in the simulation. The orientation can be
determined from the location of only 4 atoms at each time step. Other
parameters of interest can be reconstructed from the conformation of the
myosin-spin probe complex as a function of time, but with a much larger
time increment between snapshots in the md.crd file. The simulation will
have to be run out to > 10 ns. To write out an entry to a md.crd
trajectory file at each time step for analysis will generate huge files,
even if the simulation is broken up into segments. I would like to avoid
this if possible. Is there a way in Amber7 to save the coordinates of a
restricted set of four atoms at every time step, while adding a new
structure to the md.crd trajectory file at a larger increment in time?

Thank you for your help.

Ed Pate

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