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.
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 ============================================ -- 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
