Hi Itamar, I haven't really followed the discussion and I'm a bit too lazy to look it all up now ;) But have you tried setting the nst parameters to 1 (except for output). Especially nstpcouple. Note that nstpcouple=1 requires nstlist=1 and nstcalcenergy=1. If that solves the problem, you may need to extend your equilibration a bit, first relaxing NVT, followed by NPT with nstpcouple=1, thereafter equilibrating using productions conditions. It it solves it, maybe the option should be renamed nstptrouble :p
Hope it helps, Tsjerk On Thu, Sep 1, 2011 at 7:43 AM, Itamar Kass <itamar.k...@monash.edu> wrote: > HI Chris, > > I am sorry that from my mails it is seems like I am not appreciate the help, > because I appreciate it much. It is just the fact that I am trying to give as > much info as I can and to go over any idea in the mailing list without > actually delay my other stuff. So again, I wish thanks for anyone who is > helps here. > > > On 01/09/2011, at 12:20 PM, chris.ne...@utoronto.ca wrote: > >> Itamar: >> >> We really are trying to help. I think that perhaps you don't grasp how >> difficult it is to help without being able to access the simulation >> directly. Therefore we have ideas and we ask you to do specific things that >> are going to move us toward a solution, either by finding answers or by >> ruling out possibilities. >> >> It is actually useful information to know that "Sometimes it is the peptide >> N and H, like in the case of 981 and 982, and sometimes others" ... but when >> it seems like you don't want to provide the requested information my first >> inclination is to give up on trying to help. >> >> At this point, there are a few unanswered old questions and I have some new >> questions. >> >> 1. Can you reproduce this with a water box? > > The error is reproducible in a box of protein and water only. > >> 2. Can you reproduce this with your protein in vacuum? > > The error is reproduced in vacuum. > >> 3. If neither 2 or 3, then can you step slowly from one of these systems >> toward your final system and identify the point at which the lincs warnings >> arise? >> 4. Do you get the warnings without Ca also, or just with Ca? > > I am not sure what this mean. I get this warning mainly for N-H, but also for > Ca-C, pairs of atoms > >> 5. Can you reproduce this with the SD integrator? If you are really against >> trying this, then at least can you reproduce this with a single Berendsen >> temperature coupling group? > > When I use SD integrator, the simulations run fine. > >> 6. Can you reproduce this without using the reaction field? Either with PME >> or a simple cutoff? > > Using PME the system is running just fine. > >> 7. Can you trace down the version of gromacs (between 4.0.7 and 4.5.4) where >> you start to see this warning? > > I can't tell, 'cause I jump from 4.0.7 to 4.5.4. > > Thanks for the help, > Itamar > >> >> Chris. >> >> -- original message -- >> >> 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.neale at 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 at 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-request at 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.Kass at monash.edu >>>>>> ============================================ >>>>>> >>>>> -- >>>>> gmx-users mailing list gmx-users at 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-request at 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.Kass at 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 at 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-request at 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.Kass at 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 > ============================================ > > -- > 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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
