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
