Yes, I appreciate that a lot.
Song-Ho Chong
2018年9月29日(土) 1:19 James Kress <jimkress_58.kressworks.org>:
> " Anyway, it would be much nicer if round-off errors do not affect the
> elapsed time."
>
> I believe Prof. Case and the rest of the team have stated that "code
> modifications for improvement are always welcome".
>
> Jim Kress
>
> -----Original Message-----
> From: Song-Ho Chong <songho.chong.gmail.com>
> Sent: Friday, September 28, 2018 3:15 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] annoying elapsed time in mdout of amber18
>
> After reading the reply from Prof. Case and checking my simulation results
> again, I realized that this has nothing to do with the amber versions, but
> probably with the fact that, in my previous simulations I have been using
> "formatted" restart/coordinates files, whereas in my newer simulations, I'm
> using binary ones.
> (I still sometimes use formatted output files since some of in-house codes
> directly handles restart/coordinate files and they are not updated to cope
> with the binary formats.)
>
> Anyway, it would be much nicer if round-off errors do not affect the
> elapsed time.
>
> Song-Ho
>
> 2018年9月28日(金) 5:36 David Case <david.case.rutgers.edu>:
>
> > 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 like.
> >
> > 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.
> >
> > .....dac
> >
> >
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Received on Fri Sep 28 2018 - 09:30:04 PDT
