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