Re: [AMBER] annoying elapsed time in mdout of amber18

From: David Case <>
Date: Thu, 27 Sep 2018 20:36:36 +0000

On Thu, Sep 27, 2018, Song-Ho Chong wrote:

> But, for some reason, right after 336 ns production run, I see
> NSTEP = 500000 TIME(PS) = 336219.999 TEMP(K) = 309.97 PRESS = 0.0
> instead of TIME(PS) = 336220.000 that I expected.

The printed time is obtained by repeatedly adding dt to starting time, and
what you observe is an expected feature of floating point roundoff. It's not
clear why you didn't see this in earlier versions of Amber. Scripts that
process such files will need to be made aware of what the output might look

It's possible that doing something like multiplying the step number by dt,
then adding it to the starting time, would yield more pleasing-looking
results. Suggested code revisions are welcome.


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Received on Thu Sep 27 2018 - 14:00:02 PDT
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