On Sat, Oct 12, 2013 at 11:07 PM, Guillaume Chevrot < guillaume.chev...@gmail.com> wrote:
> 2013/10/12 Mark Abraham <mark.j.abra...@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? > Seems likely to me, but I would certainly try to compare apples with apples before reaching that conclusion! (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.) > Your log file has 51000 atoms (most of which are presumably water), so 4500/10/51000 is 0.0088 kJ/mol/ns/atom. 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? There are many differences in the simulations (you have protein, Fig 2 uses 2fs time steps, PME settings are different), so there is not yet any basis for assigning the reason for differences in drift. > > > > 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. The authors of that paper show Desmond's drift with RATTLE (an iterative solver), not SETTLE (a constant-time analytical solver). Desmond's drift with SETTLE would have been interesting to see. A cost/benefit analysis of simulation wall-clock time vs errors in the simulation observables for the different solvers would also be interesting. Projecting the total drift from my estimate above back onto Fig 1 of their paper is instructive ;-) > > .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 The compiler traveled on the Ark, and the binary was compiled for a machine less capable than the SSE4.1 machine you ran it on. Perhaps the compiler is correct (there are certainly known bugs in *later* gcc minor releases; get the latest), but even if the compiler is correct, you will probably observe things go faster if you fix those ;-) Mark > > Thanks for your comments! > > Guillaume > > > > > 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
