Low Soo Mei wrote:
Hi all,
I am quite new to Gromacs and would like to ask why the full _restart_
file .trr is designed such that every frame's coordinates and
velocities are retained?
It only does this if you choose to do this. See discussion here
http://wiki.gromacs.org/index.php/Doing_Restarts
In NAMD and Amber only the last frame's
coordinates and velocities are necessary for a restart. I mention this
because am wondering why it appears that the full .trr file is read when
grompping for my continuation run.
Yes, they're all read, but that's only expensive if you choose it that
way - and even then it's not much.
Unless the Gromacs analysis tools also use the .trr file for analysis,
in which case keeping data for every frame in the .trr makes more sense.
There are occasions for wanting velocities and forces over the
simulation. GROMACS allows you to decide in advance what you'll want and
to be efficient accordingly.
Mark
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