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

[Michael Shirts]

Hi, all-

At this point, any fixes are going to be in the 5.0 version, where the
integrators will be a bit different.  If you upload your system files
to redmine.gromacs.org (not just the .mdp), then I will make sure this
gets tested there.

On Fri, Oct 25, 2013 at 10:14 AM, Guillaume Chevrot
<guillaume.chevrot at gmail.com> wrote:
> Dear Xavier,
>
> 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?
>>
>>
> FYI, I tried 10 and 1 and the energy drift is exactly the same.
>
>
>
>
>>  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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