Dear Xavier, 2013/10/12 XAvier Periole <x.peri...@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.abra...@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.chev...@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.abra...@gmail.com> > >> > >>> On Oct 11, 2013 7:59 PM, "Guillaume Chevrot" < > >> guillaume.chev...@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@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-requ...@gromacs.org. > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> -- > >>> gmx-users mailing list gmx-users@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-requ...@gromacs.org. > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> -- > >> gmx-users mailing list gmx-users@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-requ...@gromacs.org. > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
