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.chev...@gmail.com> wrote: > 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 -- 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
