Re: [gmx-users] energy drift - comparison of double and single precision
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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] energy drift - comparison of double and single precision
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 listgmx-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 listgmx-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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
Re: [gmx-users] energy drift - comparison of double and single precision
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
Re: [gmx-users] energy drift - comparison of double and single precision
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 listgmx-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 listgmx-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 listgmx-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 listgmx-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.
Re: [gmx-users] energy drift - comparison of double and single precision
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? (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.) 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? 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. .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 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 listgmx-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 listgmx-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
Re: [gmx-users] energy drift - comparison of double and single precision
2013/10/12 XAvier Periole x.peri...@rug.nl Could you try to reduce the nstcalcenergy flag from 100 to 10 and then one? Thanks for the suggestion. I'll try next week and I'll show the results ASAP. Guillaume 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 listgmx-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 listgmx-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 listgmx-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
[gmx-users] energy drift - comparison of double and single precision
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. 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 -- gmx-users mailing listgmx-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
Re: [gmx-users] energy drift - comparison of double and single precision
Hi, Guillaume- No one can tell you if you did anything wrong if you didn't tell us what you did! There are literally thousands of combinations of options in running an NVE simulation, a substantial fraction of which are guaranteed not to conserve energy. If you post the files (inputs and relevant output files) to redmine.gromacs.org, then people would be able to see if it was an error in how you ran the simulation, or an actual bug. On Fri, Oct 11, 2013 at 1:58 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. 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 -- gmx-users mailing listgmx-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 listgmx-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
Re: [gmx-users] energy drift - comparison of double and single precision
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 listgmx-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 listgmx-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
Re: [gmx-users] energy drift - comparison of double and single precision
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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] energy drift - comparison of double and single precision
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 listgmx-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 listgmx-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 listgmx-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 listgmx-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
