Hi Justin, I did repeat it using gen_val and running temperature the same, with no effect, it is still crash. I didn't replied point #6 because the atoms which triggers the LINCS are different between each try. Sometimes it is the peptide N and H, like in the case of 981 and 982, and sometimes others. In addition, there is no visible difference in dynamics between 4.0.7 and 4.5.4 I can find.
Itamar On 01/09/2011, at 11:14 AM, Justin A. Lemkul wrote: > > > Itamar Kass wrote: >> Hi Mark, >> I didn't had the time to do the SD yet, but serial run end with the same >> results. I didn't try water only system, as this is of no interest to me, >> but I will simplify the system later on. > > Being of interest to you and being a useful diagnostic may be different. > It's important to rule out different variables to arrive at a solution, which > I suspect is of interest to you. You also haven't addressed points #1 and #6 > in Chris' message. > > -Justin > >> Cheers, >> Itamar >> On 01/09/2011, at 10:51 AM, Mark Abraham wrote: >>> On 1/09/2011 10:20 AM, Itamar Kass wrote: >>>> Hi Chris, >>>> >>>> Thanks for the email, I am sorry it took me some time to replay. I tried >>>> 4.5.4 again, now starting from a 5 ns simulations run using 4.0.7, and >>>> again the simulations had stopped after 1000 LINCS error (I can extend the >>>> simulations using 4.0.7). >>>> >>>> I know that gromacs stopped after 1000 LINCS, but this is usually a sign >>>> that something bad is going on in the system. >>> OK. Chris suggested a number of other strategies that will help determine >>> which aspect of 4.5.4 is behaving differently. How did those strategies >>> work out? >>> >>> Mark >>> >>>> Cheers, >>>> Itamar >>>> >>>> On 18/08/2011, at 12:03 PM, chris.ne...@utoronto.ca wrote: >>>> >>>>> OK, here's my last few ideas: >>>>> >>>>> 1. Please try to repeat this with gen_vel set to the same value as your >>>>> temperature coupling >>>>> >>>>> 2. Can you reproduce this in serial? >>>>> >>>>> 3. Can you reproduce this with the sd integrator? >>>>> >>>>> 4. Can you reproduce this with a simpler system? protein in vacuum or >>>>> just water or remove the ions, etc? >>>>> >>>>> 5. Take the output .gro from 4.0.7 that ran fine for X ns and run it >>>>> under 4.5.4. Do you get the same lincs warnings? >>>>> >>>>> 6. Also, note that you are getting warnings and the run does not actually >>>>> crash but just stops after too many warnings. So what are atoms 981 and >>>>> 982? Does their motion look different in an important ways between the >>>>> 4.0.7 and 4.5.4 trajectories? >>>>> >>>>> Chris. >>>>> >>>>> -- original message -- >>>>> >>>>> Hi Chris, >>>>> >>>>> thanks for the advice, I have to say I tried this as well without any >>>>> success. >>>>> >>>>> Itamar >>>>> >>>>> On 18/08/2011, at 11:11 AM, chris.neale at utoronto.ca wrote: >>>>> >>>>>> run an EM with flexible water. I often find that this is the only way to >>>>>> get a stable system. 500 steps of steep with define=-DFLEXIBLE (or >>>>>> different depending on your water model I think) should be enough. >>>>>> >>>>>> Chris. >>>>>> >>>>>> Hi Chris and Justin, >>>>>> >>>>>> On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: >>>>>> >>>>> -- >>>>> 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 >>>> ----- >>>> "In theory, there is no difference between theory and practice. But, in >>>> practice, there is." - Jan L.A. van de Snepscheut >>>> >>>> =========================================== >>>> | Itamar Kass, Ph.D. >>>> | Postdoctoral Research Fellow >>>> | >>>> | Department of Biochemistry and Molecular Biology >>>> | Building 77 Clayton Campus >>>> | Wellington Road >>>> | Monash University, >>>> | Victoria 3800 >>>> | Australia >>>> | >>>> | Tel: +61 3 9902 9376 >>>> | Fax: +61 3 9902 9500 >>>> | E-mail: itamar.k...@monash.edu >>>> ============================================ >>>> >>> -- >>> 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 >> ----- >> "In theory, there is no difference between theory and practice. But, in >> practice, there is." - Jan L.A. van de Snepscheut >> =========================================== >> | Itamar Kass, Ph.D. >> | Postdoctoral Research Fellow >> | >> | Department of Biochemistry and Molecular Biology >> | Building 77 Clayton Campus >> | Wellington Road >> | Monash University, >> | Victoria 3800 >> | Australia >> | >> | Tel: +61 3 9902 9376 >> | Fax: +61 3 9902 9500 >> | E-mail: itamar.k...@monash.edu >> ============================================ > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 ----- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut =========================================== | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu ============================================ -- 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
