Hi Justing, I had reinitialised the systems after the PR run but I don't think this is the origin of the error. Because the system with the Ca crashed allways in the PR state, although the systems run with 4.0.7 done it fine.
Best, Itamnar On 18/08/2011, at 10:39 AM, Justin A. Lemkul wrote: > > > I concur with what Mark suggested about in vacuo EM. I would also point out > the following problem(s): > >> and the md.mdp: > > Here you call for 300 K as the reference temperature and the temperature at > which you've equilibrated: > >> tc-grps = Protein Non-Protein >> tau-t = 0.1 0.1 ref-t = 300 300 >> ; Pressure coupling Pcoupl = berendsen >> Pcoupltype = isotropic >> ; Time constant (ps), compressibility (1/bar) and reference P (bar) >> tau_p = 1.0 >> compressibility = 4.5e-5 ref_p = 1.0 >> ; Generate velocites is on at 290K - do not get velocity from gro file. > > And here you're destroying the previous equilibration by re-generating > velocities and simultaneously generating velocities for the wrong > temperature, which may or may not induce instability into the system. > >> gen_vel = yes >> gen_temp = 290 >> gen-seed = -1 > > -Justin > > -- > ======================================== > > 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
