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

[Guillaume Chevrot]

2013/10/12 Mark Abraham <mark.j.abraham at gmail.com>

> 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.
>
>
Do you suggest that SETTLE is the cause of the drift?
(note: If I did not mistaken, my drift would be 0.18 [k_B T / ns / atom],
quite close of the figures shown in their figure 2.)
In their Figure 2, they show a drift for single and double precision, and
it is not the case for my double precision simulation, so maybe SETTLE is
no the cause of my trouble?




> Note that using md-vv guarantees the 2007 paper is inapplicable, because
> GROMACS did not have a velocity Verlet integrator back then. Sharing the
>

If I remember well, their demonstration was true whatever the integrator.
Nevertheless, I also tested the leap-frog integrator, and I observe the
same drift in energy.
So maybe their explanation is still applicable.



> .log files might be informative.
>
>
Here is the link where you can find the log file:
http://dx.doi.org/10.6084/m9.figshare.821211

Thanks for your comments!

Guillaume



> 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
> > >
> > > > --
> > > > gmx-users mailing list    gmx-users at gromacs.org
> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > > * Please don't post (un)subscribe requests to the list. Use the
> > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > --
> > > gmx-users mailing list    gmx-users at gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > * Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>