Could you try to reduce the nstcalcenergy flag from 100 to 10 and then one?
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
