[AMBER-Developers] Ascii Restart Files: precision on velocities

From: <dcerutti.rci.rutgers.edu>
Date: Mon, 7 Nov 2011 17:24:46 -0500 (EST)

I finally beat some sense into the way that mdgx is starting and stopping,
what it calls the first step, etc. Hadn't been too worried about that
when I was more interested in getting long stable runs out of it, or when
I was just accumulating everything I needed internally.

But it's alerted me to one issue, which I had foreseen but not thought
much about. The ascii restart format is much less precise on velocities
than it could be. We should be able to squeeze another factor of 20.45 in
there by encoding velocities at their internal units of A/ps rather than
scaled down by sqrt(418.4). It's really the velocities that limit the
continuity of restarts.

I suppose it's not so much an issue if we're moving towards standardized
binary restarts anyway, but how did we come up with a format that is both
cryptic and less precise than the %12.7f format can handle? I realize
that, in some case, the velocities could be any values because of some
very large random value, but the probability of getting an absolute
|velocity| > 999 A/ps has to be so remote, even at like 1500K, that it
shouldn't break the format in a lifetime of number crunching. Not meaning
to start a flame war, but just curious on this one.


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Received on Mon Nov 07 2011 - 14:30:03 PST
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