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

[Mark Abraham]

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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