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

[Guillaume Chevrot]

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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