[gmx-users] energy drift - comparison of double and single precision

[Guillaume Chevrot]

2013/10/12 XAvier Periole <x.periole at rug.nl>

>
> Could you try to reduce the nstcalcenergy flag from 100 to 10 and then one?
>
>
Thanks for the suggestion.  I'll try next week and I'll show the results
ASAP.

Guillaume




>  Similar flags apply to temperature and pressure and I believe might
> seriously affect energy conservation.
>
> XAvier.
>
> > On Oct 12, 2013, at 0:50, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> >
> > Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing)
> > 30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger
> than
> > that. I bet the rest of the lysozyme model physics is not accurate to
> less
> > than 1% ;-) There are some comparative numbers at
> > http://dx.doi.org/10.1016/j.cpc.2013.06.003 - the two systems are rather
> > different but they share the use of SETTLE.
> >
> > Note that using md-vv guarantees the 2007 paper is inapplicable, because
> > GROMACS did not have a velocity Verlet integrator back then. Sharing the
> > .log files might be informative.
> >
> > Mark
> >
> >
> > On Fri, Oct 11, 2013 at 11:38 PM, Guillaume Chevrot <
> > guillaume.chevrot at gmail.com> wrote:
> >
> >> Hi,
> >>
> >> sorry for my last post! I re-write my e-mail (with some additional
> >> information) and I provide the links to my files ;-)
> >>
> >> I compared the total energy of 2 simulations:
> >> lysozyme in water / NVE ensemble / single precision / Gromacs 4.6.3
> >> lysozyme in water / NVE ensemble / double precision / Gromacs 4.6.3
> >>
> >> ... and what I found was quite ... disturbing (see the plots of the
> total
> >> energy: http://dx.doi.org/10.6084/m9.figshare.820153). I observe a
> >> constant
> >> drift in energy in the case of the single precision simulation.
> >>
> >> Did I do something wrong*? Any remarks are welcomed! Here is the link to
> >> the ‘mdout.mdp’ file (http://dx.doi.org/10.6084/m9.figshare.820154) so
> you
> >> can check what mdp options I used.
> >>
> >> My second question is: if I did not do something wrong, what are the
> >> consequences on the simulation? Can I trust the results of single
> precision
> >> simulations?
> >>
> >> Regards,
> >>
> >> Guillaume
> >>
> >> *PS: I am not the only one encountering this behavior. In the
> literature,
> >> this problem has already been mentioned:
> >> http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1
> >>
> >>
> >>
> >>
> >> 2013/10/11 Mark Abraham <mark.j.abraham at gmail.com>
> >>
> >>> On Oct 11, 2013 7:59 PM, "Guillaume Chevrot" <
> >> guillaume.chevrot at gmail.com>
> >>> wrote:
> >>>>
> >>>> Hi all,
> >>>>
> >>>> I recently compared the total energy of 2 simulations:
> >>>> lysozyme in water / NVE ensemble / single precision
> >>>> lysozyme in water / NVE ensemble / double precision
> >>>>
> >>>> ... and what I found was quite ... disturbing (see the attached figure
> >> -
> >>>> plots of the total energy). I observe a constant drift in energy in
> the
> >>>> case of the single precision simulation.
> >>>>
> >>>> Did I do something wrong*? Any remarks are welcomed! I join the
> >>> ‘mdout.mdp’
> >>>> file so you can check what mdp options I used.
> >>>
> >>> Maybe. Unfortunately we cannot configure the mailing list to allow
> people
> >>> to send attachments to thousands of people, so you will need to do
> >>> something like provide links to files on a sharing service.
> >>>
> >>>>
> >>>> My second question is: if I did not do something wrong, what are the
> >>>> consequences on the simulation? Can I trust the results of single
> >>> precision
> >>>> simulations?
> >>>
> >>> Yes, as you have no doubt read in the papers published by the GROMACS
> >> team.
> >>>
> >>>> Regards,
> >>>>
> >>>> Guillaume
> >>>>
> >>>> *PS: I am not the only one encountering this behavior. In the
> >> literature,
> >>>> this problem has already been mentioned:
> >>>> http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1
> >>>
> >>> ... which is six years old, examining the properties of code seven
> years
> >>> old. Life has moved on! :-) Even if you have found a problem, it is a
> big
> >>> assumption that this is (still) the cause.
> >>>
> >>> Mark
> >>>
> >>>> --
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