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. 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
